Nucleic acid and corresponding protein entitled 213P1F11 useful in treatment and detection of cancer

ABSTRACT

A novel gene (designated 213P1F11) and its encoded protein, and variants thereof, are described wherein 213P1F11 exhibits tissue specific expression in normal adult tissue, and is aberrantly expressed in the cancers listed in Table I. Consequently, 213P1F11 provides a diagnostic, prognostic, prophylactic and/or therapeutic target for cancer. The 213P1F11 gene or fragment thereof, or its encoded protein, or variants thereof, or a fragment thereof, can be used to elicit a humoral or cellular immune response; antibodies or T cells reactive with 213P1F11 can be used in active or passive immunization.

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] Not applicable.

STATEMENT OF RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSOREDRESEARCH

[0002] Not applicable.

FIELD OF THE INVENTION

[0003] The invention described herein relates to a gene and its encodedprotein, termed 213P1F11, expressed in certain cancers, and todiagnostic and therapeutic methods and compositions useful in themanagement of cancers that express 213P1F11.

BACKGROUND OF THE INVENTION

[0004] Cancer is the second leading cause of human death next tocoronary disease. Worldwide, millions of people die from cancer everyyear. In the United States alone, as reported by the American CancerSociety, cancer causes the death of well over a half-million peopleannually, with over 1.2 million new cases diagnosed per year. Whiledeaths from heart disease have been declining significantly, thoseresulting from cancer generally are on the rise. In the early part ofthe next century, cancer is predicted to become the leading cause ofdeath.

[0005] Worldwide, several cancers stand out as the leading killers. Inparticular, carcinomas of the lung, prostate, breast, colon, pancreas,and ovary represent the primary causes of cancer death. These andvirtually all other carcinomas share a common lethal feature. With veryfew exceptions, metastatic disease from a carcinoma is fatal. Moreover,even for those cancer patients who initially survive their primarycancers, common experience has shown that their lives are dramaticallyaltered. Many cancer patients experience strong anxieties driven by theawareness of the potential for recurrence or treatment failure. Manycancer patients experience physical debilitations following treatment.Furthermore, many cancer patients experience a recurrence.

[0006] Worldwide, prostate cancer is the fourth most prevalent cancer inmen. In North America and Northern Europe, it is by far the most commoncancer in males and is the second leading cause of cancer death in men.In the United States alone, well over 30,000 men die annually of thisdisease—second only to lung cancer. Despite the magnitude of thesefigures, there is still no effective treatment for metastatic prostatecancer. Surgical prostatectomy, radiation therapy, hormone ablationtherapy, surgical castration and chemotherapy continue to be the maintreatment modalities. Unfortunately, these treatments are ineffectivefor many and are often associated with undesirable consequences.

[0007] On the diagnostic front, the lack of a prostate tumor marker thatcan accurately detect early-stage, localized tumors remains asignificant limitation in the diagnosis and management of this disease.Although the serum prostate specific antigen (PSA) assay has been a veryuseful tool, however its specificity and general utility is widelyregarded as lacking in several important respects.

[0008] Progress in identifying additional specific markers for prostatecancer has been improved by the generation of prostate cancer xenograftsthat can recapitulate different stages of the disease in mice. The LAPC(Los Angeles Prostate Cancer) xenografts are prostate cancer xenograftsthat have survived passage in severe combined immune deficient (SCID)mice and have exhibited the capacity to mimic the transition fromandrogen dependence to androgen independence (Klein et al., 1997, Nat.Med. 3:402). More recently identified prostate cancer markers includePCTA-1 (Su et al., 1996, Proc. Natl. Acad. Sci. USA 93: 7252),prostate-specific membrane (PSM) antigen (Pinto et al., Clin Cancer Res1996 Sep 2 (9): 1445-51), STEAP (Hubert, et al., Proc Natl Acad Sci USA.Dec. 7, 1999; 96(25): 14523-8) and prostate stem cell antigen (PSCA)(Reiter et al., 1998, Proc. Natl. Acad. Sci. USA 95: 1735).

[0009] While previously identified markers such as PSA, PSM, PCTA andPSCA have facilitated efforts to diagnose and treat prostate cancer,there is need for the identification of additional markers andtherapeutic largets for prostate and related cancers in order to furtherimprove diagnosis and therapy.

[0010] Renal cell carcinoma (RCC) accounts for approximately 3 percentof adult malignancies. Once adenomas reach a diameter of 2 to 3 cm,malignant potential exists. In the adult, the two principal malignantrenal tumors are renal cell adenocarcinoma and transitional cellcarcinoma of the renal pelvis or ureter. The incidence of renal celladenocarcinoma is estimated at more than 29,000 cases in the UnitedStates, and more than 11,600 patients died of this disease in 1998.Transitional cell carcinoma is less frequent, with an incidence ofapproximately 500 cases per year in the United States.

[0011] Surgery has been the primary therapy for renal celladenocarcinoma for many decades. Until recently, metastatic disease hasbeen refractory to any systemic therapy. With recent developments insystemic therapies, particularly immunotherapies, metastatic renal cellcarcinoma may be approached aggressively in appropriate patients with apossibility of durable responses. Nevertheless, there is a remainingneed for effective therapies for these patients.

[0012] Of all new cases of cancer in the United States, bladder cancerrepresents approximately 5 percent in men (fifth most common neoplasm)and 3 percent in women (eighth most common neoplasm). The incidence isincreasing slowly, concurrent with an increasing older population. In1998, there was an estimated 54,500 cases, including 39,500 in men and15,000 in women. The age-adjusted incidence in the United States is 32per 100,000 for men and 8 per 100,000 in women. The historic male/femaleratio of 3:1 may be decreasing related to smoking patterns in women.There were an estimated 11,000 deaths from bladder cancer in 1998 (7,800in men and 3,900 in women). Bladder cancer incidence and mortalitystrongly increase with age and will be an increasing problem as thepopulation becomes more elderly.

[0013] Most bladder cancers recur in the bladder. Bladder cancer ismanaged with a combination of transurethral resection of the bladder(TUR) and intravesical chemotherapy or immunotherapy. The multifocal andrecurrent nature of bladder cancer points out the limitations of TUR.Most muscle-invasive cancers are not cured by TUR alone. Radicalcystectomy and urinary diversion is the most effective means toeliminate the cancer but carry an undeniable impact on urinary andsexual function. There continues to be a significant need for treatmentmodalities that are beneficial for bladder cancer patients.

[0014] An estimated 130,200 cases of colorectal cancer occurred in 2000in the United States, including 93,800 cases of colon cancer and 36,400of rectal cancer. Colorectal cancers are the third most common cancersin men and women. Incidence rates declined significantly during1992-1996 (−2.1% per year). Research suggests that these declines havebeen due to increased screening and polyp removal, preventingprogression of polyps to invasive cancers. There were an estimated56,300 deaths (47,700 from colon cancer, 8,600 from rectal cancer) in2000, accounting for about 11% of all U.S. cancer deaths.

[0015] At present, surgery is the most common form of therapy forcolorectal cancer, and for cancers that have not spread, it isfrequently curative. Chemotherapy, or chemotherapy plus radiation, isgiven before or after surgery to most patients whose cancer has deeplyperforated the bowel wall or has spread to the lymph nodes. A permanentcolostomy (creation of an abdominal opening for elimination of bodywastes) is occasionally needed for colon cancer and is infrequentlyrequired for rectal cancer. There continues to be a need for effectivediagnostic and treatment modalities for colorectal cancer.

[0016] There were an estimated 164,100 new cases of lung and bronchialcancer in 2000, accounting for 14% of all U.S. cancer diagnoses. Theincidence rate of lung and bronchial cancer is declining significantlyin men, from a high of 86.5 per 100,000 in 1984 to 70.0 in 1996. In the1990s, the rate of increase among women began to slow. In 1996, theincidence rate in women was 42.3 per 100,000.

[0017] Lung and bronchial cancer caused an estimated 156,900 deaths in2000, accounting for 28% of all cancer deaths. During 1992-1996,mortality from lung cancer declined significantly among men (−1.7% peryear) while rates for women were still significantly increasing (0.9%per year). Since 1987, more women have died each year of lung cancerthan breast cancer, which, for over 40 years, was the major cause ofcancer death in women. Decreasing lung cancer incidence and mortalityrates most likely resulted from decreased smoking rates over theprevious 30 years; however, decreasing smoking patterns among women lagbehind those of men. Of concern, although the declines in adult tobaccouse have slowed, tobacco use in youth is increasing again.

[0018] Treatment options for lung and bronchial cancer are determined bythe type and stage of the cancer and include surgery, radiation therapy,and chemotherapy. For many localized cancers, surgery is usually thetreatment of choice. Because the disease has usually spread by the timeit is discovered, radiation therapy and chemotherapy are often needed incombination with surgery. Chemotherapy alone or combined with radiationis the treatment of choice for small cell lung cancer; on this regimen,a large percentage of patients experience remission, which in some casesis long lasting. There is however, an ongoing need for effectivetreatment and diagnostic approaches for lung and bronchial cancers.

[0019] An estimated 182,800 new invasive cases of breast cancer wereexpected to occur among women in the United States during 2000.Additionally, about 1,400 new cases of breast cancer were expected to bediagnosed in men in 2000. After increasing about 4% per year in the1980s, breast cancer incidence rates in women have leveled off in the1990s to about 110.6 cases per 100,000.

[0020] In the U.S. alone, there were an estimated 41,200 deaths (40,800women, 400 men) in 2000 due to breast cancer. Breast cancer ranks secondamong cancer deaths in women. According to the most recent data,mortality rates declined significantly during 1992-1996 with the largestdecreases in younger women, both white and black. These decreases wereprobably the result of earlier detection and improved treatment.

[0021] Taking into account the medical circumstances and the patient'spreferences, treatment of breast cancer may involve lumpectomy (localremoval of the tumor) and removal of the lymph nodes under the arm;mastectomy (surgical removal of the breast) and removal of the lymphnodes under the arm; radiation therapy; chemotherapy; or hormonetherapy. Often, two or more methods are used in combination. Numerousstudies have shown that, for early stage disease, long-term survivalrates after lumpectomy plus radiotherapy are similar to survival ratesafter modified radical mastectomy. Significant advances inreconstruction techniques provide several options for breastreconstruction after mastectomy. Recently, such reconstruction has beendone at the same time as the mastectomy.

[0022] Local excision of ductal carcinoma in situ (DCIS) with adequateamounts of surrounding normal breast tissue may prevent the localrecurrence of the DCIS. Radiation to the breast and/or tamoxifen mayreduce the chance of DCIS occurring in the remaining breast tissue. Thisis important because DCIS, if left untreated, may develop into invasivebreast cancer. Nevertheless, there are serious side effects or sequelaeto these treatments. There is, therefore, a need for efficacious breastcancer treatments.

[0023] There were an estimated 23,100 new cases of ovarian cancer in theUnited States in 2000. It accounts for 4% of all cancers among women andranks second among gynecologic cancers. During 1992-1996, ovarian cancerincidence rates were significantly declining. Consequent to ovariancancer, there were an estimated 14,000 deaths in 2000. Ovarian cancercauses more deaths than any other cancer of the female reproductivesystem.

[0024] Surgery, radiation therapy, and chemotherapy are treatmentoptions for ovarian cancer. Surgery usually includes the removal of oneor both ovaries, the fallopian tubes (salpingo-oophorectomy), and theuterus (hysterectomy). In some very early tumors, only the involvedovary will be removed, especially in young women who wish to havechildren. In advanced disease, an attempt is made to remove allintra-abdominal disease to enhance the effect of chemotherapy. Therecontinues to be an important need for effective treatment options forovarian cancer.

[0025] There were an estimated 28,300 new cases of pancreatic cancer inthe United States in 2000. Over the past 20 years, rates of pancreaticcancer have declined in men. Rates among women have remainedapproximately constant but may be beginning to decline. Pancreaticcancer caused an estimated 28,200 deaths in 2000 in the United States.Over the past 20 years, there has been a slight but significant decreasein mortality rates among men (about −0.9% per year) while rates haveincreased slightly among women.

[0026] Surgery, radiation therapy, and chemotherapy are treatmentoptions for pancreatic cancer. These treatment options can extendsurvival and/or relieve symptoms in many patients but are not likely toproduce a cure for most. There is a significant need for additionaltherapeutic and diagnostic options for pancreatic cancer.

SUMMARY OF THE INVENTION

[0027] The present invention relates to a gene, designated 213P1F11,that has now been found to be over-expressed in the cancer(s) listed inTable I. Northern blot expression analysis of 213P1F11 gene expressionin normal tissues shows a restricted expression pattern in adulttissues. The nucleotide (FIG. 2) and amino acid (FIG. 2, and FIG. 3)sequences of 213P1F11 are provided. The tissue-related profile of213P1F11 in normal adult tissues, combined with the over-expressionobserved in the tissues listed in Table I, shows that 213P1F11 isaberrantly over-expressed in at least some cancers, and thus serves as auseful diagnostic, prophylactic, prognostic, and/or therapeutic targetfor cancers of the tissue(s) such as those listed in Table I.

[0028] The invention provides polynucleotides corresponding orcomplementary to all or part of the 213P1F11 genes, mRNAs, and/or codingsequences, preferably in isolated form, including polynucleotidesencoding 213P1F11-related proteins and fragments of 4, 5, 6, 7, 8, 9,10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or morethan 25 contiguous amino acids; at least 30, 35, 40, 45, 50, 55, 60, 65,70, 80, 85, 90, 95, 100 or more than 100 contiguous amino acids of a213P1F11-related protein, as well as the peptides/proteins themselves;DNA, RNA, DNA/RNA hybrids, and related molecules, polynucleotides oroligonucleotides complementary or having at least a 90% homology to the213P1F11 genes or mRNA sequences or parts thereof, and polynucleotidesor oligonucleotides that hybridize to the 213P1F11 genes, mRNAs, or to213P1F11-encoding polynucleotides. Also provided are means for isolatingcDNAs and the genes encoding 213P1F11. Recombinant DNA moleculescontaining 213P1F11 polynucleotides, cells transformed or transducedwith such molecules, and host-vector systems for the expression of213P1F11 gene products are also provided. The invention further providesantibodies that bind to 213P1F11 proteins and polypeptide fragmentsthereof, including polyclonal and monoclonal antibodies, murine andother mammalian antibodies, chimeric antibodies, humanized and fullyhuman antibodies, and antibodies labeled with a detectable marker ortherapeutic agent. In certain embodiments there is a proviso that theentire nucleic acid sequence of FIG. 2 is not encoded and/or the entireamino acid sequence of FIG. 2 is not prepared. In certain embodiments,the entire nucleic acid sequence of FIG. 2 is encoded and/or the entireamino acid sequence of FIG. 2 is prepared, either of which are inrespective human unit dose forms.

[0029] The invention further provides methods for detecting the presenceand status of 213P1F11 polynucleotides and proteins in variousbiological samples, as well as methods for identifying cells thatexpress 213P1F11. A typical embodiment of this invention providesmethods for monitoring 213P1F11 gene products in a tissue or hematologysample having or suspected of having some form of growth dysregulationsuch as cancer.

[0030] The invention further provides various immunogenic or therapeuticcompositions and strategies for treating cancers that express 213P1F11such as cancers of tissues listed in Table I, including therapies aimedat inhibiting the transcription, translation, processing or function of213P1F11 as well as cancer vaccines. In one aspect, the inventionprovides compositions, and methods comprising them, for treating acancer that expresses 213P1F11 in a human subject wherein thecomposition comprises a carrier suitable for human use and a human unitdose of one or more than one agent that inhibits the production orfunction of 213P1F11. Preferably, the carrier is a uniquely humancarrier. In another aspect of the invention, the agent is a moiety thatis immunoreactive with 213P1F11 protein. Non-limiting examples of suchmoieties include, but are not limited to, antibodies (such as singlechain, monoclonal, polyclonal, humanized, chimeric, or humanantibodies), functional equivalents thereof (whether naturally occurringor synthetic), and combinations thereof. The antibodies can beconjugated to a diagnostic or therapeutic moiety. In another aspect, theagent is a small molecule as defined herein.

[0031] In another aspect, the agent comprises one or more than onepeptide which comprises a cytotoxic T lymphocyte (CTL) epitope thatbinds an HLA class I molecule in a human to elicit a CTL response to213P1F11 and/or one or more than one peptide which comprises a helper Tlymphocyte (HTL) epitope which binds an HLA class II molecule in a humanto elicit an HTL response. The peptides of the invention may be on thesame or on one or more separate polypeptide molecules. In a furtheraspect of the invention, the agent comprises one or more than onenucleic acid molecule that expresses one or more than one of the CTL orHTL response stimulating peptides as described above. In yet anotheraspect of the invention, the one or more than one nucleic acid moleculemay express a moiety that is immunologically reactive with 213P1F11 asdescribed above. The one or more than one nucleic acid molecule may alsobe, or encodes, a molecule that inhibits production of 213P1F11.Non-limiting examples of such molecules include, but are not limited to,those complementary to a nucleotide sequence essential for production of213P1F11 (e.g. antisense sequences or molecules that form a triple helixwith a nucleotide double helix essential for 213P1F11 production) or aribozyme effective to lyse 213P1F11 mRNA.

BRIEF DESCRIPTION OF THE FIGURES

[0032]FIG. 1. The 213P1F11 SSH sequence of 166 nucleotides.

[0033]FIG. 2. The cDNA (SEQ ID. NO.:______) and amino acid sequence (SEQID. NO.:______) of 213P1F11 variant 1 clone CASP14-BrCl (also called“213P1F11 v.1” or “213P1F11 variant 1” or “213P1F11”) is shown in FIG.2A. The start methionine is underlined. The open reading frame extendsfrom nucleic acid 404-1132 including the stop codon. The cDNA (SEQ ID.NO.:______) and amino acid sequence (SEQ ID. NO.:______) of 213P1F11variant 2 (also called “213P1F11 v.2”) is shown in FIG. 2B. The codonfor the start methionine is underlined. The open reading frame extendsfrom nucleic acid 409-1096 including the stop codon. The cDNA (SEQ ID.NO.:______) and amino acid sequence (SEQ ID. NO.:______) of 213P1F11variant 3 (also called “213P1F11 v.3”) is shown in FIG. 2C. The codonfor the start methionine is underlined. The open reading frame extendsfrom nucleic acid 404-844 including the stop codon. The cDNA (SEQ ID.NO.:______) and amino acid sequence (SEQ ID. NO.:______) of 213P1F11variant 4 (also called “213P1F11 v.4”) is shown in FIG. 2D. The codonfor the start methionine is underlined. The open reading frame extendsfrom nucleic acid 1-966 including the stop codon. The cDNA (SEQ ID.NO.:______) and amino acid sequence (SEQ ID. NO.:______) of 213P1F11variant 5 (also called “213P1F11 v.5”) is shown in FIG. 2E. The codonfor the start methionine is underlined. The open reading frame extendsfrom nucleic acid 404-1132 including the stop codon. The cDNA (SEQ ID.NO.:______) and amino acid sequence (SEQ ID. NO.:______) of 213P1F11variant 6 (also called “213P1F11 variant v.6”) is shown in FIG. 2F. Thecodon for the start methionine is underlined. The open reading frameextends from nucleic acid 404-1132 including the stop codon. The cDNA(SEQ ID. NO.:______) and amino acid sequence (SEQ ID. NO.:______) of213P1F11 variant 7 (also called “213P1F11 v.7”) is shown in FIG. 2G. Thecodon for the start methionine is underlined. The open reading frameextends from nucleic acid 404-1132 including the stop codon. The cDNA(SEQ ID. NO.:______) and amino acid sequence (SEQ ID. NO.:______) of213P1F11 variant 8 (also called “213P1F11 v.8”) is shown in FIG. 2H. Thecodon for the start methionine is underlined. The open reading frameextends from nucleic acid 404-1132 including the stop codon. As usedherein, a reference to 213P1F11 includes all variants thereof, includingthose shown in FIG. 10.

[0034]FIG. 3. Amino acid sequence of 213P1F11 v.1 (SEQ ID. NO.:______)is shown in FIG. 3A; it has 242 amino acids. The amino acid sequence of213P1F11 v.2 (SEQ ID. NO.:______) is shown in FIG. 3B; it has 230 aminoacids. The amino acid sequence of 213P1F11 v.3 (SEQ ID. NO.:______) isshown in FIG. 3C; it has 146 amino acids. The amino acid sequence of213P1F11 v.4 (SEQ ID. NO.:______) is shown in FIG. 3D; it has 321 aminoacids. The amino acid sequence of 213P1F11 v.5 (SEQ ID. NO.:______) isshown in FIG. 3E; it has 242 amino acids. The amino acid sequence of213P1F11 v.6 (SEQ ID. NO.:______) is shown in FIG. 3F; it has 242 aminoacids. As used herein, a reference to 213P1F11 includes all variantsthereof, including those shown in FIG. 11.

[0035]FIG. 4. The nucleic acid sequence alignment of 213P1F11 v.1 withhuman Caspase-14 (gi 6912286)precursor mRNA is shown in FIG. 4A. Theamino acid sequence alignment of 213P1F11 v.1 with human Caspase-14 (gi6912286) mRNA is shown in FIG. 4B. The amino acid sequence alignment of213P1F11 v.1 with mouse Caspase-14 (gi 6753280) mRNA is shown in FIG.4C. The amino acid sequence alignment of 213P1F11 v.2 with humanCaspase-14 (gi 6912286) mRNA is shown in FIG. 4D. The amino acidsequence alignment of 213P1F11 v.3 with human Caspase-14 (gi 6912286)mRNA is shown in FIG. 4E. The amino acid sequence alignment of 213P1F11v.2 with mouse caspase 14 (gi 6753280) mRNA is shown in FIG. 4F. Theamino acid sequence alignment of 213P1F11 v.4 with human Caspase-14 (gi6912286) mRNA is shown in FIG. 4G.

[0036]FIG. 5. Hydrophilicity amino acid profile of A) 213P1F11 variant1, B) 213P1F11 variant 2, C) 213P1F11 variant 3 and D) 213P1F11 variant4, determined by computer algorithm sequence analysis using the methodof Hopp and Woods (Hopp T. P., Woods K. R., 1981. Proc. Natl. Acad. Sci.U.S.A. 78:3824-3828) accessed on the Protscale website(www.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecularbiology server.

[0037]FIG. 6. Hydropathicity amino acid profile of A) 213P1F11 variant1, B) 213P1F11 variant 2, C) 213P1F11 variant 3 and D) 213P1F11 variant4, determined by computer algorithm sequence analysis using the methodof Kyte and Doolittle (Kyte J., Doolittle R. F., 1982. J. Mol. Biol.157:105-132) accessed on the ProtScale website(www.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecularbiology server.

[0038]FIG. 7. Percent accessible residues amino acid profile of A)213P1F11 variant 1, B) 213P1F11 variant 2, C) 213P1F11 variant 3 and D)213P1F11 variant 4, determined by computer algorithm sequence analysisusing the method of Janin (Janin J., 1979 Nature 277:491-492) accessedon the ProtScale website (www.expasy.ch/cgi-bin/protscale.pl) throughthe ExPasy molecular biology server.

[0039]FIG. 8. Average flexibility amino acid profile of A) 213P1F11variant 1, B) 213P1F11 variant 2, C) 213P1F11 variant 3 and D) 213P1F11variant 4, determined by computer algorithm sequence analysis using themethod of Bhaskaran and Ponnuswamy (Bhaskaran R., and Ponnuswamy P. K.,1988. Int. J. Pept. Protein Res. 32:242-255) accessed on the ProtScalewebsite (www.expasy.ch/cgi-bin/protscale.pl) through the ExPasymolecular biology server.

[0040]FIG. 9. Beta-turn amino acid profile of A) 213P1F11 variant 1, B)213P1F11 variant 2, C) 213P1F11 variant 3 and D) 213P1F11 variant 4,determined by computer algorithm sequence analysis using the method ofDeleage and Roux (Deleage, G., Roux B. 1987 Protein Engineering1:289-294) accessed on the ProtScale website(www.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecularbiology server.

[0041]FIG. 10. Schematic display of nucleotide variants of 213P1F11.Variants 213P1F11 v.2 and v.3 are splice variants. Variant 213P1F11 v.4is an alternative transcript. Others are Single Nucleotide Polymorphism(also called “SNP”) variants, which could also occur in any of thetranscript variants that contains the base pairs. Numbers in “( )”underneath the box correspond to those of 213P1F11 v.1. The black boxesshow the same sequence as 213P1F11 v.1. SNPs are indicated above thebox.

[0042]FIG. 11. Schematic display of protein variants of 213P1F11.Nucleotide variants 213P1F11 v.1 though v.6 in FIG. 10 code for proteinvariants 213P1F11 v.1 through 213P1F11 v.6, respectively. Variants213P1F11 v.7 through v.10 code the same protein as variant 213P1F11 v.1.Protein variants 213P1F11 v.5 and v.6 are variants with single aminoacid variations, which may exist in transcript variants 213P1F11 v.2through 4. The black boxes show the same sequence as 213P1F11 v.1. Thenumbers in “( )” underneath the box correspond to those of 213P1F11 v.1.Single amino acid differences are indicated above the box.

[0043]FIG. 12. Secondary structure prediction for 213P1F11 variants 1through 4. The secondary structures of 213P1F11 variant 1 (A), variant 2(B), variant 3 (C), and variant 4 (D) were predicted using theHNN—Hierarchical Neural Network method (Guermeur, 1997,http://pbil.ibcp.fr/cgi-bin/npsa automat.pl?page=npsa_nn.html), accessedfrom the ExPasy molecular biology server (http://www.expasy.ch/tools/).This method predicts the presence and location of alpha helices,extended strands, and random coils from the primary protein sequence.The percent of the protein in a given secondary structure is also listedfor each variant.

[0044]FIG. 13. Exon compositions of transcript variants of 213P11F11.Variant 213P1F11 v.2 and v.3 are splice variants. Variant 213P1F11 v.4is an alternative transcript. Compared with 213P1F11 v.1, 213P1F11 v.2has a longer (+74 bp at 5′ end) exon 6 and variant 213P1F11 v.3 has alonger (+68 bp at 5′ end) exon 5. Variant 213P1F11 v.4 has threedifferent exons. Relative locations of exons from all variants on thechromosome are shown at the bottom. Numbers in “( )” underneath the boxcorrespond to those of 213P1F11 v.1. Black boxes show the same sequenceas 213P1F11 v.1. Intron lengths are not proportional.

[0045]FIG. 14. Expression of 213P1F11 by RT-PCR. First strand cDNA wasprepared from vital pool 1 (liver, lung and kidney), vital pool 2(pancreas, colon and stomach), LAPC xenograft pool (LAPC-4AD, LAPC-4AI,LAPC-9AD and LAPC-9AI), bladder cancer pool, breast cancer pool, andcancer metastasis pool. Normalization was performed by PCR using primersto actin and GAPDH. Semi-quantitative PCR, using primers to 213P1F11,was performed at 26 and 30 cycles of amplification. Results show strongexpression of 213P1F11 in bladder cancer pool, breast cancer pool,xenograft pool, and cancer metastasis pool.

[0046]FIG. 15. Expression of 213P1F11 v.1 compared to 213P1F11 v.2 inpatient cancer samples by RT-PCR. To determine the relative expressionof 213P1F11 v.1 compared to 213P1F11 v.2 in human cancers, primers weredesigned flanking the insertion in 213P1F11 v.2. Using these primers,amplification of 213P1F11 v.1 will generate a PCR fragment of 165 bp,whereas 213P1F11 v.2 will generate a PCR fragment of 249 bp as depictedin the figure. First strand cDNA was prepared from vital pool 1 (liver,lung and kidney), bladder cancer pool, breast cancer pool, LAPCxenograft pool (LAPC-4AD, LAPC-4AI, LAPC-9AD and LAPC-9AI), and 213P1F11v.1 plasmid control. Normalization was performed by PCR using primers toactin and GAPDH. Semi-quantitative PCR, using primers depicted above,was performed at 35 cycles of amplification. Results show strongexpression of 213P1F11 v.1 in bladder cancer pool, breast cancer pool,LAPC xenograft pool, and the plasmid positive control. A lowerexpression of the 249 bp 213P1F11 v.2 product was detected in breastcancer pool, LAPC xenograft pool, and to lower extent in bladder cancerpool.

[0047]FIG. 16. Expression of 213P1F11 in normal tissues. Three multipletissue northern blots (A and B, Clontech; C, OriGene) with 2 ug ofmRNA/lane were probed with the 213P1F11 SSH fragment. Size standards inkilobases (kb) are indicated on the side. Results show strong expressionof 213P1F11 only in skin tissue. A weak transcript is detected in normalthymus but not in the other tissues tested.

[0048]FIG. 17. Expression of 213P1F11 in bladder cancer patient tissues.RNA was extracted from normal bladder (N), bladder cancer cell lines(UM-UC-3 and SCaBER), bladder cancer patient tumors (T) and normaltissue adjacent to bladder cancer (N_(AT)). Northern blots with 10 ug oftotal RNA were probed with the 213P1F11 SSH fragment. Size standards inkilobases are indicated on the side. Results show strong expression of213P1F11 in the bladder tumor tissues but not in normal bladder nor inthe bladder cancer cell lines.

[0049]FIG. 18. Expression of 213P1F11 in prostate cancer xenografts. RNAwas extracted from normal prostate, LAPC-4AD, LAPC-4AI, LAPC-9AD andLAPC-9AI prostate cancer xenografts. Northern blot with 10 μg of totalRNA/lane was probed with 213P1F11 SSH sequence. Size standards inkilobases (kb) are indicated on the side. The results show expression of213P1F11 in the LAPC-9AI xenograft, but not in the other xenografts norin normal prostate.

[0050]FIG. 19. Expression of 213P1F11 in breast cancer patient tissues.RNA was extracted from normal breast (N), breast cancer cell lines(DU4475, MCF7 and CAMA-1), breast cancer patient tumors (T) and breastcancer metastasis to lymph node (Met). Northern blots with 10 ug oftotal RNA were probed with the 213P1F11 SSH fragment. Size standards inkilobases are indicated on the side. Results show strong expression of213P1F11 in the breast tumor tissues as well as in the cancer metastasisspecimen. Weak expression was also detected in the CAMA-1 cell line, butnot in the other 2 breast cancer cell lines tested.

DETAILED DESCRIPTION OF THE INVENTION

[0051] Outline of Sections

[0052] I.) Definitions

[0053] II.) 213P1F11 Polynucleotides

[0054] II.A.) Uses of 213P1F11 Polynucleotides

[0055] II.A.1.) Monitoring of Genetic Abnormalities

[0056] II.A.2.) Antisense Embodiments

[0057] II.A.3.) Primers and Primer Pairs

[0058] II.A.4.) Isolation of 213P1F11-Encoding Nucleic Acid Molecules

[0059] I.A.5.) Recombinant Nucleic Acid Molecules and Host-VectorSystems

[0060] III.) 213P1F11-related Proteins

[0061] III.A.) Motif-bearing Protein Embodiments

[0062] III.B.) Expression of 213P1F11-related Proteins

[0063] III.C.) Modifications of 213P1F11-related Proteins

[0064] III.D.) Uses of 213P1F11-related Proteins

[0065] IV.) 213P1F11 Antibodies

[0066] V.) 213P1F11 Cellular Immune Responses

[0067] VI.) 213P1F11 Transgenic Animals

[0068] VII.) Methods for the Detection of 213P1F11

[0069] VIII.) Methods for Monitoring the Status of 213P1F11-relatedGenes and Their Products

[0070] IX.) Identification of Molecules That Interact With 213P1F11

[0071] X.) Therapeutic Methods and Compositions

[0072] X.A.) Anti-Cancer Vaccines

[0073] X.B.) 213P1F11 as a Target for Antibody-Based Therapy

[0074] X.C.) 213P1F11 as a Target for Cellular Immune Responses

[0075] X.C.1. Minigene Vaccines

[0076] X.C.2. Combinations of CTL Peptides with Helper Peptides

[0077] X.C.3. Combinations of CTL Peptides with T Cell Priming Agents

[0078] X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL and/orHTL Peptides

[0079] X.D.) Adoptive Immunotherapy

[0080] X.E.) Administration of Vaccines for Therapeutic or ProphylacticPurposes

[0081] XI.) Diagnostic and Prognostic Embodiments of 213P1F11.

[0082] XII.) Inhibition of 213P1F11 Protein Function

[0083] XII.A.) Inhibition of 213P1F11 With Intracellular Antibodies

[0084] XII.B.) Inhibition of 213P1F11 with Recombinant Proteins

[0085] XII.C.) Inhibition of 213P1F11 Transcription or Translation

[0086] XII.D.) General Considerations for Therapeutic Strategies

[0087] XIII.) KITS

[0088] I.) Definitions:

[0089] Unless otherwise defined, all terms of art, notations and otherscientific terms or terminology used herein are intended to have themeanings commonly understood by those of skill in the art to which thisinvention pertains. In some cases, terms with commonly understoodmeanings are defined herein for clarity and/or for ready reference, andthe inclusion of such definitions herein should not necessarily beconstrued to represent a substantial difference over what is generallyunderstood in the art. Many of the techniques and procedures describedor referenced herein are well understood and commonly employed usingconventional methodology by those skilled in the art, such as, forexample, the widely utilized molecular cloning methodologies describedin Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd. edition(1989) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. Asappropriate, procedures involving the use of commercially available kitsand reagents are generally carried out in accordance with manufacturerdefined protocols and/or parameters unless otherwise noted.

[0090] The terms “advanced prostate cancer”, “locally advanced prostatecancer”, “advanced disease” and “locally advanced disease” mean prostatecancers that have extended through the prostate capsule, and are meantto include stage C disease under the American Urological Association(AUA) system, stage C1-C2 disease under the Whitmore-Jewett system, andstage T3-T4 and N+ disease under the TNM (tumor, node, metastasis)system. In general, surgery is not recommended for patients with locallyadvanced disease, and these patients have substantially less favorableoutcomes compared to patients having clinically localized(organ-confined) prostate cancer. Locally advanced disease is clinicallyidentified by palpable evidence of induration beyond the lateral borderof the prostate, or asymmetry or induration above the prostate base.Locally advanced prostate cancer is presently diagnosed pathologicallyfollowing radical prostatectomy if the tumor invades or penetrates theprostatic capsule, extends into the surgical margin, or invades theseminal vesicles.

[0091] “Altering the native glycosylation paftem” is intended forpurposes herein to mean deleting one or more carbohydrate moieties foundin native sequence 213P1F11 (either by removing the underlyingglycosylation site or by deleting the glycosylation by chemical and/orenzymatic means), and/or adding one or more glycosylation sites that arenot present in the native sequence 213P1F11. In addition, the phraseincludes qualitative changes in the glycosylation of the nativeproteins, involving a change in the nature and proportions of thevarious carbohydrate moieties present.

[0092] The term “analog” refers to a molecule which is structurallysimilar or shares similar or corresponding attributes with anothermolecule (e.g. a 213P1F11-related protein). For example an analog of a213P1F11 protein can be specifically bound by an antibody or T cell thatspecifically binds to 213P1F11.

[0093] The term “antibody” is used in the broadest sense. Therefore an“antibody” can be naturally occurring or man-made such as monoclonalantibodies produced by conventional hybridoma technology. Anti-213P1F11antibodies comprise monoclonal and polyclonal antibodies as well asfragments containing the antigen-binding domain and/or one or morecomplementarity determining regions of these antibodies.

[0094] An “antibody fragment” is defined as at least a portion of thevariable region of the immunoglobulin molecule that binds to its target,i.e., the antigen-binding region. In one embodiment it specificallycovers single anti-213P1F11 antibodies and clones thereof (includingagonist, antagonist and neutralizing antibodies) and anti-213P1F11antibody compositions with polyepitopic specificity.

[0095] The term “codon optimized sequences” refers to nucleotidesequences that have been optimized for a particular host species byreplacing any codons having a usage frequency of less than about 20%.Nucleotide sequences that have been optimized for expression in a givenhost species by elimination of spurious polyadenylation sequences,elimination of exon/intron splicing signals, elimination oftransposon-like repeats and/or optimization of GC content in addition tocodon optimization are referred to herein as an “expression enhancedsequences.”

[0096] The term “cytotoxic agent” refers to a substance that inhibits orprevents the expression activity of cells, function of cells and/orcauses destruction of cells. The term is intended to include radioactiveisotopes chemotherapeutic agents, and toxins such as small moleculetoxins or enzymatically active toxins of bacterial, fungal, plant oranimal origin, including fragments and/or variants thereof Examples ofcytotoxic agents include, but are not limited to maytansinoids, yttrium,bismuth, ricin, ricin A-chain, doxorubicin, daunorubicin, taxol,ethidium bromide, mitomycin, etoposide, tenoposide, vincristine,vinblastine, colchicine, dihydroxy anthracin dione, actinomycin,diphtheria toxin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin Achain, modeccin A chain, alpha-sarcin, gelonin, mitogellin,retstrictocin, phenomycin, enomycin, curicin, crotin, calicheamicin,sapaonaria officinalis inhibitor, and glucocorticoid and otherchemotherapeutic agents, as well as radioisotopes such as At²¹¹, I¹³¹,I¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, Bi²¹², P³² and radioactive isotopes ofLu. Antibodies may also be conjugated to an anti-cancer pro-drugactivating enzyme capable of converting the pro-drug to its active form.

[0097] The term “homolog” refers to a molecule which exhibits homologyto another molecule, by for example, having sequences of chemicalresidues that are the same or similar at corresponding positions.

[0098] “Human Leukocyte Antigen” or “HLA” is a human class I or class IIMajor Histocompatibility Complex (MHC) protein (see, e.g., Stites, etal., IMMUNOLOGY, 8^(TH) ED., Lange Publishing, Los Altos, Calif. (1994).

[0099] The terms “hybridize”, “hybridizing”, “hybridizes” and the like,used in the context of polynucleotides, are meant to refer toconventional hybridization conditions, preferably such as hybridizationin 50% formamide/6×SSC/0.1% SDS/100 μg/ml ssDNA, in which temperaturesfor hybridization are above 37 degrees C. and temperatures for washingin 0.1× SSC/0.1% SDS are above 55 degrees C.

[0100] The phrases “isolated” or “biologically pure” refer to materialwhich is substantially or essentially free from components whichnormally accompany the material as it is found in its native state.Thus, isolated peptides in accordance with the invention preferably donot contain materials normally associated with the peptides in their insitu environment. For example, a polynucleotide is said to be “isolated”when it is substantially separated from contaminant polynucleotides thatcorrespond or are complementary to genes other than the 213P1F11 genesor that encode polypeptides other than 213P1F11 gene product orfragments thereof. A skilled artisan can readily employ nucleic acidisolation procedures to obtain an isolated 213P1F11 polynucleotide. Aprotein is said to be “isolated,” for example, when physical, mechanicalor chemical methods are employed to remove the 213P1F11 proteins fromcellular constituents that are normally associated with the protein. Askilled artisan can readily employ standard purification methods toobtain an isolated 213P1F11 protein. Alternatively, an isolated proteincan be prepared by chemical means.

[0101] The term “mammal” refers to any organism classified as a mammal,including mice, rats, rabbits, dogs, cats, cows, horses and humans. Inone embodiment of the invention, the mammal is a mouse. In anotherembodiment of the invention, the mammal is a human.

[0102] The terms “metastatic prostate cancer” and “metastatic disease”mean prostate cancers that have spread to regional lymph nodes or todistant sites, and are meant to include stage D disease under the AUAsystem and stage T×N×M+ under the TNM system. As is the case withlocally advanced prostate cancer, surgery is generally not indicated forpatients with metastatic disease, and hormonal (androgen ablation)therapy is a preferred treatment modality. Patients with metastaticprostate cancer eventually develop an androgen-refractory state within12 to 18 months of treatment initiation. Approximately half of theseandrogen-refractory patients die within 6 months after developing thatstatus. The most common site for prostate cancer metastasis is bone.Prostate cancer bone metastases are often osteoblastic rather thanosteolytic (i.e., resulting in net bone formation). Bone metastases arefound most frequently in the spine, followed by the femur, pelvis, ribcage, skull and humerus. Other common sites for metastasis include lymphnodes, lung, liver and brain. Metastatic prostate cancer is typicallydiagnosed by open or laparoscopic pelvic lymphadenectomy, whole bodyradionuclide scans, skeletal radiography, and/or bone lesion biopsy.

[0103] The term “monoclonal antibody” refers to an antibody obtainedfrom a population of substantially homogeneous antibodies, i.e., theantibodies comprising the population are identical except for possiblenaturally occurring mutations that are present in minor amounts.

[0104] A “motif”, as in biological motif of a 213P1F11-related protein,refers to any pattern of amino acids forming part of the primarysequence of a protein, that is associated with a particular function(e.g. protein-protein interaction, protein-DNA interaction, etc) ormodification (e.g. that is phosphorylated, glycosylated or amidated), orlocalization (e.g. secretory sequence, nuclear localization sequence,etc.) or a sequence that is correlated with being immunogenic, eitherhumorally or cellularly. A motif can be either contiguous or capable ofbeing aligned to certain positions that are generally correlated with acertain function or property. In the context of HLA motifs, “motif”refers to the pattern of residues in a peptide of defined length,usually a peptide of from about 8 to about 13 amino acids for a class IHLA motif and from about 6 to about 25 amino acids for a class II HLAmotif, which is recognized by a particular HLA molecule. Peptide motifsfor HLA binding are typically different for each protein encoded by eachhuman HLA allele and differ in the pattern of the primary and secondaryanchor residues.

[0105] A “pharmaceutical excipient” comprises a material such as anadjuvant, a carrier, pH-adjusting and buffering agents, tonicityadjusting agents, wetting agents, preservative, and the like.

[0106] “Pharmaceutically acceptable” refers to a non-toxic, inert,and/or composition that is physiologically compatible with humans orother mammals.

[0107] The term “polynucleotide” means a polymeric form of nucleotidesof at least 10 bases or base pairs in length, either ribonucleotides ordeoxynucleotides or a modified form of either type of nucleotide, and ismeant to include single and double stranded forms of DNA and/or RNA. Inthe art, this term if often used interchangeably with “oligonucleotide”.A polynucleotide can comprise a nucleotide sequence disclosed hereinwherein thymidine (T), as shown for example in FIG. 2, can also beuracil (U); this definition pertains to the differences between thechemical structures of DNA and RNA, in particular the observation thatone of the four major bases in RNA is uracil (U) instead of thymidine(T).

[0108] The term “polypeptide” means a polymer of at least about 4, 5, 6,7, or 8 amino acids. Throughout the specification, standard three letteror single letter designations for amino acids are used. In the art, thisterm is often used interchangeably with “peptide” or “protein”.

[0109] An HLA “primary anchor residue” is an amino acid at a specificposition along a peptide sequence which is understood to provide acontact point between the immunogenic peptide and the HLA molecule. Oneto three, usually two, primary anchor residues within a peptide ofdefined length generally defines a “motif” for an immunogenic peptide.These residues are understood to fit in close contact with peptidebinding groove of an HLA molecule, with their side chains buried inspecific pockets of the binding groove. In one embodiment, for example,the primary anchor residues for an HLA class I molecule are located atposition 2 (from the amino terminal position) and at the carboxylterminal position of a 8, 9, 10, 11, or 12 residue peptide epitope inaccordance with the invention. In another embodiment, for example, theprimary anchor residues of a peptide that will bind an HLA class IImolecule are spaced relative to each other, rather than to the terminiof a peptide, where the peptide is generally of at least 9 amino acidsin length. The primary anchor positions for each motif and supermotifare set forth in Table IV. For example, analog peptides can be createdby altering the presence or absence of particular residues in theprimary and/or secondary anchor positions shown in Table IV. Suchanalogs are used to modulate the binding affinity and/or populationcoverage of a peptide comprising a particular HLA motif or supermotif.

[0110] A “recombinant” DNA or RNA molecule is a DNA or RNA molecule thathas been subjected to molecular manipulation in vitro.

[0111] Non-limiting examples of small molecules include compounds thatbind or interact with 213P1F11, ligands including hormones,neuropeptides, chemokines, odorants, phospholipids, and functionalequivalents thereof that bind and preferably inhibit 213P1F11 proteinfunction. Such non-limiting small molecules preferably have a molecularweight of less than about 10 kDa, more preferably below about 9, about8, about 7, about 6, about 5 or about 4 kDa. In certain embodiments,small molecules physically associate with, or bind, 213P1F11 protein;are not found in naturally occurring metabolic pathways; and/or are moresoluble in aqueous than non-aqueous solutions “Stringency” ofhybridization reactions is readily determinable by one of ordinary skillin the art, and generally is an empirical calculation dependent uponprobe length, washing temperature, and salt concentration. In general,longer probes require higher temperatures for proper annealing, whileshorter probes need lower temperatures. Hybridization generally dependson the ability of denatured nucleic acid sequences to reanneal whencomplementary strands are present in an environment below their meltingtemperature. The higher the degree of desired homology between the probeand hybridizable sequence, the higher the relative temperature that canbe used. As a result, it follows that higher relative temperatures wouldtend to make the reaction conditions more stringent, while lowertemperatures less so. For additional details and explanation ofstringency of hybridization reactions, see Ausubel et al., CurrentProtocols in Molecular Biology, Wiley Interscience Publishers, (1995).

[0112] “Stringent conditions” or “high stringency conditions”, asdefined herein, are identified by, but not limited to, those that: (1)employ low ionic strength and high temperature for washing, for example0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium dodecylsulfate at 50° C.; (2) employ during hybridization a denaturing agent,such as formamide, for example, 50% (v/v) formamide with 0.1% bovineserum albumin/0.1% Ficoll/0.1% polyvinylpyrrolidone/50 mM sodiumphosphate buffer at pH 6.5 with 750 mM sodium chloride, 75 mM sodiumcitrate at 42° C.; or (3) employ 50% formamide, 5×SSC (0.75 M NaCl,0.075 M sodium citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodiumpyrophosphate, 5× Denhardt's solution, sonicated salmon sperm DNA (50μg/ml), 0.1% SDS, and 10% dextran sulfate at 42° C., with washes at 42°C. in 0.2×SSC (sodium chloride/sodium. citrate) and 50% formamide at 55°C., followed by a high-stringency wash consisting of 0.1×SSC containingEDTA at 55° C. “Moderately stringent conditions” are described by, butnot limited to, those in Sambrook et al., Molecular Cloning: ALaboratory Manual, New York: Cold Spring Harbor Press, 1989, and includethe use of washing solution and hybridization conditions (e.g.,temperature, ionic strength and %SDS) less stringent than thosedescribed above. An example of moderately stringent conditions isovernight incubation at 37° C. in a solution comprising: 20% formamide,5×SSC (150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5× Denhardt's solution, 10% dextran sulfate, and 20 mg/mLdenatured sheared salmon sperm DNA, followed by washing the filters in1×SSC at about 37-50° C. The skilled artisan will recognize how toadjust the temperature, ionic strength, etc. as necessary to accommodatefactors such as probe length and the like.

[0113] An HLA “supermotif” is a peptide binding specificity shared byHLA molecules encoded by two or more HLA alleles.

[0114] As used herein “to treat” or “therapeutic” and grammaticallyrelated terms, refer to any improvement of any consequence of disease,such as prolonged survival, less morbidity, and/or a lessening of sideeffects which are the byproducts of an alternative therapeutic modality;full eradication of disease is not required.

[0115] A “transgenic animal” (e.g., a mouse or rat) is an animal havingcells that contain a transgene, which transgene was introduced into theanimal or an ancestor of the animal at a prenatal, e.g., an embryonicstage. A “transgene” is a DNA that is integrated into the genome of acell from which a transgenic animal develops.

[0116] As used herein, an HLA or cellular immune response “vaccine” is acomposition that contains or encodes one or more peptides of theinvention. There are numerous embodiments of such vaccines, such as acocktail of one or more individual peptides; one or more peptides of theinvention comprised by a polyepitopic peptide; or nucleic acids thatencode such individual peptides or polypeptides, e.g., a minigene thatencodes a polyepitopic peptide. The “one or more peptides” can includeany whole unit integer from 1-242 or more, e.g., at least 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28,29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100,105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170,175, 180, 185, 190, 195, 200, 225, or 242 or more peptides of theinvention. The peptides or polypeptides can optionally be modified, suchas by lipidation, addition of targeting or other sequences. HLA class Ipeptides of the invention can be admixed with, or linked to, HLA classII peptides, to facilitate activation of both cytotoxic T lymphocytesand helper T lymphocytes. HLA vaccines can also comprise peptide-pulsedantigen presenting cells, e.g., dendritic cells.

[0117] The term “variant” refers to a molecule that exhibits a variationfrom a described type or norm, such as a protein that has one or moredifferent amino acid residues in the corresponding position(s) of aspecifically described protein (e.g. the 213P1F11 protein shown in FIG.2 or FIG. 3. An analog is an example of a variant protein. Spliceisofomis and single nucleotides polymorphisms (SNPs) are furtherexamples of variants.

[0118] The “213P1F11-related proteins” of the invention include thosespecifically identified herein, as well as allelic variants,conservative substitution variants, analogs and homologs that can beisolated/generated and characterized without undue experimentationfollowing the methods outlined herein or readily available in the art.Fusion proteins that combine parts of different 213P1F11 proteins orfragments thereof, as well as fusion proteins of a 213P1F11 protein anda heterologous polypeptide are also included. Such 213P1F11 proteins arecollectively referred to as the 213P1F11-related proteins, the proteinsof the invention, or 213P1F11. The term “213P1F11-related protein”refers to a polypeptide fragment or a 213P1F11 protein sequence of 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, or more than 25 amino acids; or, at least 30, 35,40, 45, 50, 55, 60,65, 70, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140,145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, or 242or more amino acids.

[0119] II.) 213P1F11 Polynucleotides

[0120] One aspect of the invention provides polynucleotidescorresponding or complementary to all or part of a 213P1F11 gene, mRNA,and/or coding sequence, preferably in isolated form, includingpolynucleotides encoding a 213P1F11-related protein and fragmentsthereof, DNA, RNA, DNA/RNA hybrid, and related molecules,polynucleotides or oligonucleotides complementary to a 213P1F11 gene ormRNA sequence or a part thereof, and polynucleotides or oligonucleotidesthat hybridize to a 213P1F11 gene, mRNA, or to a 213P1F11 encodingpolynucleotide (collectively, “213P1F11 polynucleotides”). In allinstances when referred to in this section, T can also be U in FIG. 2.

[0121] Embodiments of a 213P1F11 polynucleotide include: a 213P1F11polynucleotide having the sequence shown in FIG. 2, the nucleotidesequence of 213P1F11 as shown in FIG. 2 wherein T is U; at least 10contiguous nucleotides of a polynucleotide having the sequence as shownin FIG. 2; or, at least 10 contiguous nucleotides of a polynucleotidehaving the sequence as shown in FIG. 2 where T is U. For example,embodiments of 213P1F11 nucleotides comprise, without limitation:

[0122] (I) a polynucleotide comprising, consisting essentially of, orconsisting of a sequence as shown in FIG. 2 (SEQ ID NO:______), whereinT can also be U;

[0123] (II) a polynucleotide comprising, consisting essentially of, orconsisting of the sequence as shown in FIG. 2 (SEQ ID NO:______), fromnucleotide residue number 404 through nucleotide residue number 1132,including the stop codon, wherein T can also be U;

[0124] (III) a polynucleotide comprising, consisting essentially of, orconsisting of the sequence as shown in FIG. 2B (SEQ ID NO:______), fromnucleotide residue number 404 through nucleotide residue number 1096,including the stop codon, wherein T can also be U;

[0125] (IV) a polynucleotide comprising, consisting essentially of, orconsisting of the sequence as shown in FIG. 2C (SEQ ID NO:______), fromnucleotide residue number 404 through nucleotide residue number 844,including the a stop codon, wherein T can also be U;

[0126] (V) a polynucleotide comprising, consisting essentially of, orconsisting of the sequence as shown in FIG. 2D (SEQ ID NO:______), fromnucleotide residue number 1 through nucleotide residue number 966,including the stop codon, wherein T can also be U;

[0127] (VI) a polynucleotide comprising, consisting essentially of, orconsisting of the sequence as shown in FIG. 2E (SEQ ID NO:______), fromnucleotide residue number 404 through nucleotide residue number 1132,including the stop codon, wherein T can also be U;

[0128] (VII) a polynucleotide comprising, consisting essentially of, orconsisting of the sequence as shown in FIG. 2F (SEQ ID NO:______), fromnucleotide residue number 404 through nucleotide residue number 1132,including the stop codon, wherein T can also be U;

[0129] (VIII) a polynucleotide comprising, consisting essentially of, orconsisting of the sequence as shown in FIG. 2G (SEQ ID NO:______), fromnucleotide residue number 404 through nucleotide residue number 1132,including the stop codon, wherein T can also be U;

[0130] (IX) a polynucleotide comprising, consisting essentially of, orconsisting of the sequence as shown in FIG. 2H (SEQ ID NO:______), fromnucleotide residue number 404 through nucleotide residue number 1132,including the stop codon, wherein T can also be U;

[0131] (X) a polynucleotide that encodes a 213P1F11-related protein thatis at least 90% homologous to an entire amino acid sequence shown inFIGS. 2A-H (SEQ ID NO:______);

[0132] (XI) a polynucleotide that encodes a 213P1F11-related proteinthat is at least 90% identical to an entire amino acid sequence shown inFIGS. 2A-H (SEQ ID NO:______);

[0133] (XII) a polynucleotide that encodes at least one peptide setforth in Tables V-XIX;

[0134] (XIII) a polynucleotide that encodes a peptide region of at least5 amino acids of a peptide of FIG. 3A in any whole number increment upto 242 that includes an amino acid position having a value greater than0.5 in the Hydrophilicity profile of FIG. 5A; or of FIG. 3B in any wholenumber increment up to 230 that includes an amino acid position having avalue greater than 0.5 in the Hydrophilicity profile of FIG. 5B; or ofFIG. 3C in any whole number increment up to 146 that includes an aminoacid position having a value greater than 0.5 in the Hydrophilicityprofile of FIG. 5C; or of FIG. 3D in any whole number increment up to321 that includes an amino acid position having a value greater than 0.5in the Hydrophilicity profile of FIG. 5D;

[0135] (XIV) a polynucleotide that encodes a peptide region of at least5 amino acids of a peptide of FIG. 3A in any whole number increment upto 242 that includes an amino acid position having a value less than 0.5in the Hydropathicity profile of FIG. 6A; or of FIG. 3B in any wholenumber increment up to 230 that includes an amino acid position having avalue less than 0.5 in the Hydropathicity profile of FIG. 6B; or of FIG.3C in any whole number increment up to 146 that includes an amino acidposition having a value less than 0.5 in the Hydropathicity profile ofFIG. 6C; or of FIG. 3D in any whole number increment up to 321 thatincludes an amino acid position having a value less than 0.5 in theHydropathicity profile of FIG. 6D;

[0136] (XV) a polynucleotide that encodes a peptide region of at least 5amino acids of a peptide of FIG. 3A in any whole number increment up to242 that includes an amino acid position having a value greater than 0.5in the Percent Accessible Residues profile of FIG. 7A; or of FIG. 3B inany whole number increment up to 230 that includes an amino acidposition having a value greater than 0.5 in the Percent AccessibleResidues profile of FIG. 7B; or of FIG. 3C in any whole number incrementup to 146 that includes an amino acid position having a value greaterthan 0.5 in the Percent Accessible Residues profile of FIG. 7C; or ofFIG. 3D in any whole number increment up to 321 that includes an aminoacid position having a value greater than 0.5 in the Percent AccessibleResidues profile of FIG. 7D;

[0137] (XVI) a polynucleotide that encodes a peptide region of at least5 amino acids of a peptide of FIG. 3A in any whole number increment upto 242 that includes an amino acid position having a value greater than0.5 in the Average Flexibility profile of FIG. 8A; or of FIG. 3B in anywhole number increment up to 230 that includes an amino acid positionhaving a value greater than 0.5 in the Average Flexibility profile ofFIG. 8B; or of FIG. 3C in any whole number increment up to 146 thatincludes an amino acid position having a value greater than 0.5 in theAverage Flexibility profile of FIG. 8C; or of FIG. 3D in any wholenumber increment up to 321 that includes an amino acid position having avalue greater than 0.5 in the Average Flexibility profile of FIG. 8D;

[0138] (XVII) a polynucleotide that encodes a peptide region of at least5 amino acids of a peptide of FIG. 3A in any whole number increment upto 242 that includes an amino acid position having a value greater than0.5 in the Beta-turn profile of FIG. 9A; or of FIG. 3B in any wholenumber increment up to 230 that includes an amino acid position having avalue greater than 0.5 in the Beta-turn profile of FIG. 9B; or of FIG.3C in any whole number increment up to 146 that includes an amino acidposition having a value greater than 0.5 in the Beta-turn profile ofFIG. 9C; or of FIG. 3D in any whole number increment up to 321 thatincludes an amino acid position having a value greater than 0.5 in theBeta-turn profile of FIG. 9D;

[0139] (XVIII) a polynucleotide that is fully complementary to apolynucleotide of any one of (I)-(XVII).

[0140] (XIX) a peptide that is encoded by any of (I)-(XVIII); and

[0141] (XXI) a polynucleotide of any of (I)-(XVIII) or peptide of (XIX)together with a pharmaceutical excipient and/or in a human unit doseform.

[0142] As used herein, a range is understood to specifically discloseall whole unit positions thereof.

[0143] Typical embodiments of the invention disclosed herein include213P1F11 polynucleotides that encode specific portions of 213P1F11 mRNAsequences (and those which are complementary to such sequences) such asthose that encode the proteins and/or fragments thereof, for example:

[0144] (a) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90,95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160,165, 170, 175, 180, 185, 190, 195, 200, 225, 230, 235, 240, or 242 ormore contiguous amino acids of 213P1F11.

[0145] (b) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, 30, 35,40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90,95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160,165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225, or 230contiguous amino acids of variant 2;

[0146] (c) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90,95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, or 146 contiguousamino acids of variant 3; or

[0147] (d) 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90,95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, or 146 150, 155,160, 165, 170, 175, 180, 185, 190, 195, 200, 205, 210, 215, 220, 225,230, 235, 240, 245, 250, 255, 260, 265, 270, 275, 280, 285, 290, 295,300, 305, 310, 315, 320, or 321 contiguous amino acids of variant 4.

[0148] For example, representative embodiments of the inventiondisclosed herein include: polynucleotides and their encoded peptidesthemselves encoding about amino acid 1 to about amino acid 10 of the213P1F11 protein shown in FIG. 2 or FIG. 3, polynucleotides encodingabout amino acid 10 to about amino acid 20 of the 213P1F11 protein shownin FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 20 toabout amino acid 30 of the 213P1F11 protein shown in FIG. 2 or FIG. 3,polynucleotides encoding about amino acid 30 to about amino acid 40 ofthe 213P1F11 protein shown in FIG. 2 or FIG. 3, polynucleotides encodingabout amino acid 40 to about amino acid 50 of the 213P1F11 protein shownin FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 50 toabout amino acid 60 of the 213P1F11 protein shown in FIG. 2 or FIG. 3,polynucleotides encoding about amino acid 60 to about amino acid 70 ofthe 213P1F11 protein shown in FIG. 2 or FIG. 3, polynucleotides encodingabout amino acid 70 to about amino acid 80 of the 213P1F11 protein shownin FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 80 toabout amino acid 90 of the 213P1F11 protein shown in FIG. 2 or FIG. 3,polynucleotides encoding about amino acid 90 to about amino acid 100 ofthe 213P1F11 protein shown in FIG. 2 or FIG. 3, in increments of about10 amino acids, ending at the carboxyl terminal amino acid set forth inFIG. 2 or FIG. 3. Accordingly polynucleotides encoding portions of theamino acid sequence (of about 10 amino acids), of amino acids 100through the carboxyl terminal amino acid of the 213P1F11 protein areembodiments of the invention. Wherein it is understood that eachparticular amino acid position discloses that position plus or minusfive amino acid residues.

[0149] Polynucleotides encoding relatively long portions of a 213P1F11protein are also within the scope of the invention. For example,polynucleotides encoding from about amino acid 1 (or 20 or 30 or 40etc.) to about amino acid 20, (or 30, or 40 or 50 etc.) of the 213P1F11protein “or variant” shown in FIG. 2 or FIG. 3 can be generated by avariety of techniques well known in the art. These polynucleotidefragments can include any portion of the 213P1F11 sequence as shown inFIG. 2.

[0150] Additional illustrative embodiments of the invention disclosedherein include 213P1F11 polynucleotide fragments encoding one or more ofthe biological motifs contained within a 213P1F11 protein “or variant”sequence, including one or more of the motif-bearing subsequences of a213P1F11 protein “or variant” set forth in Tables V-XIX.

[0151] Note that to determine the starting position of any peptide setforth in Tables V-XIX (collectively HLA Peptide Tables) respective toits parental protein, e.g., variant 1, variant 2, etc., reference ismade to three factors: the particular variant, the length of the peptidein an HLA Peptide Table, and the Search Peptides in Table XXIX.Generally, a unique Search Peptide is used to obtain HLA peptides of aparticular for a particular variant. The position of each Search Peptiderelative to its respective parent molecule is listed in Table XXIX.Accordingly if a Search Peptide begins at position “X”, one must add thevalue “X−1” to each position in Tables V-XIX to obtain the actualposition of the HLA peptides in their parental molecule. For example ifa particular Search Peptide begins at position 150 of is parentalmolecule, one must add 150−1, i.e., 149 to each HLA peptide amino acidposition to calculate the position of that amino acid in the parentmolecule.

[0152] One embodiment of the invention comprises an HLA peptide, thatoccurs at least twice in Tables V-XIX collectively, or anoligonucleotide that encodes the HLA peptide. Another embodiment of theinvention comprises an HLA peptide that occurs at least once in TablesV-XVIII and at least once in table XIX, or an oligonucleotide thatencodes the HLA peptide.

[0153] Another embodiment of the invention is antibody epitopes whichcomprise a peptide regions, or an oligonucleotide encoding the peptideregion, that has one two, three, four, or five of the followingcharacteristics:

[0154] i) a peptide region of at least 5 amino acids of a particularpeptide of FIG. 3, in any whole number increment up to the full lengthof that protein in FIG. 3, that includes an amino acid position having avalue equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having avalue equal to 1.0, in the Hydrophilicity profile of FIG. 5;

[0155] ii) a peptide region of at least 5 amino acids of a particularpeptide of FIG. 3, in any whole number increment up to the full lengthof that protein in FIG. 3, that includes an amino acid position having avalue equal to or less than 0.5, 0.4, 0.3, 0.2, 0.1, or having a valueequal to 0.0, in the Hydropathicity profile of FIG. 6;

[0156] iii) a peptide region of at least 5 amino acids of a particularpeptide of FIG. 3, in any whole number increment up to the full lengthof that protein in FIG. 3, that includes an amino acid position having avalue equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having avalue equal to 1.0, in the Percent Accessible Residues profile of FIG.7;

[0157] iv) a peptide region of at least 5 amino acids of a particularpeptide of FIG. 3, in any whole number increment up to the full lengthof that protein in FIG. 3, that includes an amino acid position having avalue equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having avalue equal to 1.0, in the Average Flexibility profile of FIG. 8; or

[0158] v) a peptide region of at least 5 amino acids of a particularpeptide of FIG. 3, in any whole number increment up to the full lengthof that protein in FIG. 3, that includes an amino acid position having avalue equal to or greater than 0.5, 0.6, 0.7, 0.8, 0.9, or having avalue equal to 1.0, in the Beta-turn profile of FIG. 9.

[0159] In another embodiment, typical polynucleotide fragments of theinvention encode one or more of the regions of 213P1F11 protein orvariant that exhibit homology to a known molecule. In another embodimentof the invention, typical polynucleotide fragments can encode one ormore of the 213P1F11 protein or variant N-glycosylation sites, cAMP andcGMP-dependent protein kinase phosphorylation sites, casein kinase IIphosphorylation sites or N-myristoylation site and amidation sites.

[0160] II.A.) Uses of 213P1F11 Polynucleotides

[0161] II.A.1.) Monitoring of Genetic Abnormalities

[0162] The polynucleotides of the preceding paragraphs have a number ofdifferent specific uses. The human 213P1F11 gene maps to the chromosomallocation set forth in the Example entitled “Chromosomal Mapping of213P1F11.” For example, because the 213P1F11 gene maps to thischromosome, polynucleotides that encode different regions of the213P1F11 proteins are used to characterize cytogenetic abnormalities ofthis chromosomal locale, such as abnormalities that are identified asbeing associated with various cancers. In certain genes, a variety ofchromosomal abnormalities including rearrangements have been identifiedas frequent cytogenetic abnormalities in a number of different cancers(see e.g. Krajinovic et al, Mutat. Res. 382(3-4): 81-83 (1998);Johansson et al, Blood 86(10): 3905-3914 (1995) and Finger et al,P.N.A.S. 85(23): 9158-9162 (1988)). Thus, polynucleotides encodingspecific regions of the 213P1F11 proteins provide new tools that can beused to delineate, with greater precision than previously possible,cytogenetic abnormalities in the chromosomal region that encodes213P1F11 that may contribute to the malignant phenotype. In thiscontext, these polynucleotides satisfy a need in the art for expandingthe sensitivity of chromosomal screening in order to identify moresubtle and less common chromosomal abnormalities (see e.g. Evans et al.,Am. J. Obstet. Gynecol 171(4): 1055-1057 (1994)).

[0163] Furthermore, as 213P1F11 was shown to be highly expressed inbladder and other cancers, 213P1F11 polynucleotides are used in methodsassessing the status of 213P1F11 gene products in normal versuscancerous tissues. Typically, polynucleotides that encode specificregions of the 213P1F11 proteins are used to assess the presence ofperturbations (such as deletions, insertions, point mutations, oralterations resulting in a loss of an antigen etc.) in specific regionsof the 213P1F11 gene, such as regions containing one or more motifs.Exemplary assays include both RT-PCR assays as well as single-strandconformation polymorphism (SSCP) analysis (see, e.g., Marrogi et al, J.Cutan. Pathol. 26(8): 369-378 (1999), both of which utilizepolynucleotides encoding specific regions of a protein to examine theseregions within the protein.

[0164] II.A.2.) Antisense Embodiments

[0165] Other specifically contemplated nucleic acid related embodimentsof the invention disclosed herein are genomic DNA, cDNAs, ribozymes, andantisense molecules, as well as nucleic acid molecules based on analternative backbone, or including alternative bases, whether derivedfrom natural sources or synthesized, and include molecules capable ofinhibiting the RNA or protein expression of 213P1F11. For example,antisense molecules can be RNAs or other molecules, including peptidenucleic acids (PNAs) or non-nucleic acid molecules such asphosphorothioate derivatives, that specifically bind DNA or RNA in abase pair-dependent manner. A skilled artisan can readily obtain theseclasses of nucleic acid molecules using the 213P1F11 polynucleotides andpolynucleotide sequences disclosed herein.

[0166] Antisense technology entails the administration of exogenousoligonucleotides that bind to a target polynucleotide located within thecells. The term “antisense” refers to the fact that sucholigonucleotides are complementary to their intracellular targets, e.g.,213P1F11. See for example, Jack Cohen, Oligodeoxynucleotides, AntisenseInhibitors of Gene Expression, CRC Press, 1989; and Synthesis 1: 1-5(1988). The 213P1F11 antisense oligonucleotides of the present inventioninclude derivatives such as S-oligonucleotides (phosphorothioatederivatives or S-oligos, see, Jack Cohen, supra), which exhibit enhancedcancer cell growth inhibitory action. S-oligos (nucleosidephosphorothioates) are isoelectronic analogs of an oligonucleotide(O-oligo) in which a nonbridging oxygen atom of the phosphate group isreplaced by a sulfur atom. The S-oligos of the present invention can beprepared by treatment of the corresponding O-oligos with3H-1,2-benzodithiol-3-one-1,1-dioxide, which is a sulfur transferreagent. See, e.g., Iyer, R. P. et al., J. Org. Chem. 55:4693-4698(1990); and Iyer, R. P. et al, J. Am. Chem. Soc. 112:1253-1254 (1990).Additional 213P1F11 antisense oligonucleotides of the present inventioninclude morpholino antisense oligonucleotides known in the art (see,e.g., Partridge et al, 1996, Antisense & Nucleic Acid Drug Development6: 169-175).

[0167] The 213P1F11 antisense oligonucleotides of the present inventiontypically can be RNA or DNA that is complementary to and stablyhybridizes with the first 100 5′ codons or last 100 3′ codons of a213P1F11 genomic sequence or the corresponding mRNA. Absolutecomplementarity is not required, although high degrees ofcomplementarity are preferred. Use of an oligonucleotide complementaryto this region allows for the selective hybridization to 213P1F11 mRNAand not to mRNA specifying other regulatory subunits of protein kinase.In one embodiment, 213P1F11 antisense oligonucleotides of the presentinvention are 15 to 30-mer fragments of the antisense DNA molecule thathave a sequence that hybridizes to 213P1F11 mRNA. Optionally, 213P1F11antisense oligonucleotide is a 30-mer oligonucleotide that iscomplementary to a region in the first 10 5′ codons or last 10 3′ codonsof 213P1F11. Alternatively, the antisense molecules are modified toemploy ribozymes in the inhibition of 213P1F11 expression, see, e.g., L.A. Couture & D. T. Stinchcomb; Trends Genet 12: 510-515 (1996).

[0168] II.A.3.) Primers and Primer Pairs

[0169] Further specific embodiments of this nucleotides of the inventioninclude primers and primer pairs, which allow the specific amplificationof polynucleotides of the invention or of any specific parts thereof,and probes that selectively or specifically hybridize to nucleic acidmolecules of the invention or to any part thereof. Probes can be labeledwith a detectable marker, such as, for example, a radioisotope,fluorescent compound, bioluminescent compound, a chemiluminescentcompound, metal chelator or enzyme. Such probes and primers are used todetect the presence of a 213P1F11 polynucleotide in a sample and as ameans for detecting a cell expressing a 213P1F11 protein.

[0170] Examples of such probes include polypeptides comprising all orpart of the human 213P1F11 cDNA sequence shown in FIG. 2. Examples ofprimer pairs capable of specifically amplifying 213P1F11 mRNAs are alsodescribed in the Examples. As will be understood by the skilled artisan,a great many different primers and probes can be prepared based on thesequences provided herein and used effectively to amplify and/or detecta 213P1F11 mRNA.

[0171] The 213P1F11 polynucleotides of the invention are useful for avariety of purposes, including but not limited to their use as probesand primers for the amplification and/or detection of the 213P1F11gene(s), mRNA(s), or fragments thereof; as reagents for the diagnosisand/or prognosis of prostate cancer and other cancers; as codingsequences capable of directing the expression of 213P1F11 polypeptides;as tools for modulating or inhibiting the expression of the 213P1F11gene(s) and/or translation of the 213P1F11 transcript(s); and astherapeutic agents.

[0172] The present invention includes the use of any probe as describedherein to identify and isolate a 213P1F11 or 213P1F11 related nucleicacid sequence from a naturally occurring source, such as humans or othermammals, as well as the isolated nucleic acid sequence per se, whichwould comprise all or most of the sequences found in the probe used.

[0173] II.A.4.) Isolation of 213P1F11-Encoding Nucleic Acid Molecules

[0174] The 213P1F11 cDNA sequences described herein enable the isolationof other polynucleotides encoding 213P F11 gene product(s), as well asthe isolation of polynucleotides encoding 213P1F11 gene producthomologs, alternatively spliced isoforms, allelic variants, and mutantforms of a 213P1F11 gene product as well as polynucleotides that encodeanalogs of 213P1F11-related proteins. Various molecular cloning methodsthat can be employed to isolate full length cDNAs encoding a 213P1F11gene are well known (see, for example, Sambrook, J. et al, MolecularCloning: A Laboratory Manual, 2d edition, Cold Spring Harbor Press, NewYork, 1989; Current Protocols in Molecular Biology. Ausubel et al.,Eds., Wiley and Sons, 1995). For example, lambda phage cloningmethodologies can be conveniently employed, using commercially availablecloning systems (e.g., Lambda ZAP Express, Stratagene). Phage clonescontaining 213P F11 gene cDNAs can be identified by probing with alabeled 213P1F11 cDNA or a fragment thereof. For example, in oneembodiment, a 213P1F11 cDNA (e.g., FIG. 2) or a portion thereof can besynthesized and used as a probe to retrieve overlapping and fill-lengthcDNAs corresponding to a 213P1F11 gene. A 213P1F11 gene itself can beisolated by screening genomic DNA libraries, bacterial artificialchromosome libraries (BACs), yeast artificial chromosome libraries(YACs), and the like, with 213P1F11 DNA probes or primers.

[0175] II.A.5.) Recombinant Nucleic Acid Molecules and Host-VectorSystems

[0176] The invention also provides recombinant DNA or RNA moleculescontaining a 213P1F11 polynucleotide, a fragment, analog or homologuethereof, including but not limited to phages, plasmids, phagemids,cosmids, YACs, BACs, as well as various viral and non-viral vectors wellknown in the art, and cells transformed or transfected with suchrecombinant DNA or RNA molecules. Methods for generating such moleculesare well known (see, for example, Sambrook et al., 1989, supra).

[0177] The invention further provides a host-vector system comprising arecombinant DNA molecule containing a 213P1F11 polynucleotide, fragment,analog or homologue thereof within a suitable prokaryotic or eukaryotichost cell. Examples of suitable eukaryotic host cells include a yeastcell, a plant cell, or an animal cell, such as a mammalian cell or aninsect cell (e.g., a baculovirus-infectible cell such as an Sf9 orHighFive cell). Examples of suitable mammalian cells include variousprostate cancer cell lines such as DU145 and TsuPr1, other transfectableor transducible prostate cancer cell lines, primary cells (PrEC), aswell as a number of mammalian cells routinely used for the expression ofrecombinant proteins (e.g., COS, CHO, 293, 293T cells). Moreparticularly, a polynucleotide comprising the coding sequence of213P1F11 or a fragment, analog or homolog thereof can be used togenerate 213P1F11 proteins or fragments thereof using any number ofhost-vector systems routinely used and widely known in the art.

[0178] A wide range of host-vector systems suitable for the expressionof 213P1F11 proteins or fragments thereof are available, see forexample, Sambrook et al., 1989, supra; Current Protocols in MolecularBiology, 1995, supra). Preferred vectors for mammalian expressioninclude but are not limited to pcDNA 3.1 myc-His-tag (Invitrogen) andthe retroviral vector pSRatkneo (Muller et al., 1991, MCB 11:1785).(Using these expression vectors, 213P1F11 can be expressed in severalprostate cancer and non-prostate cell lines, including for example 293,293T, rat-1, NIH 3T3 and TsuPr1. The host-vector systems of theinvention are useful for the production of a 213P1F11 protein orfragment thereof. Such host-vector systems can be employed to study thefunctional properties of 213P1F11 and 213P1F11 mutations or analogs.

[0179] Recombinant human 213P1F11 protein or an analog or homolog orfragment thereof can be produced by mammalian cells transfected with aconstruct encoding a 213P1F11-related nucleotide. For example, 293Tcells can be transfected with an expression plasmid encoding 213P1F11 orfragment, analog or homolog thereof, a 213P1F11-related protein isexpressed in the 293T cells, and the recombinant 213P1F11 protein isisolated using standard purification methods (e.g., affinitypurification using anti-213P1F11 antibodies). In another embodiment, a213P1F11 coding sequence is subcloned into the retroviral vectorpSRαMSVtkneo and used to infect various mammalian cell lines, such asNIH 3T3, TsuPr1, 293 and rat-1 in order to establish 213P1F11 expressingcell lines. Various other expression systems well known in the art canalso be employed. Expression constructs encoding a leader peptide joinedin frame to a 213P1P11 coding sequence can be used for the generation ofa secreted form of recombinant 213P1F11 protein.

[0180] As discussed herein, redundancy in the genetic code permitsvariation in 213P1F11 gene sequences. In particular, it is known in theart that specific host species often have specific codon preferences,and thus one can adapt the disclosed sequence as preferred for a desiredhost. For example, preferred analog codon sequences typically have rarecodons (i.e., codons having a usage frequency of less than about 20% inknown sequences of the desired host) replaced with higher frequencycodons. Codon preferences for a specific species are calculated, forexample, by utilizing codon usage tables available on the INTERNET suchas at URL www.dna.affrc.gojp/˜nakamura/codon.html.

[0181] Additional sequence modifications are known to enhance proteinexpression in a cellular host. These include elimination of sequencesencoding spurious polyadenylation signals, exon/intron splice sitesignals, transposon-like repeats, and/or other such well-characterizedsequences that are deleterious to gene expression. The GC content of thesequence is adjusted to levels average for a given cellular host, ascalculated by reference to known genes expressed in the host cell. Wherepossible, the sequence is modified to avoid predicted hairpin secondarymRNA structures. Other useful modifications include the addition of atranslational initiation consensus sequence at the start of the openreading frame, as described in Kozak, Mol. Cell Biol., 9:5073-5080(1989). Skilled artisans understand that the general rule thateukaryotic ribosomes initiate translation exclusively at the 5′ proximalAUG codon is abrogated only under rare conditions (see, e.g., Kozak PNAS92(7): 2662-2666, (1995) and Kozak NAR 15(20): 8125-8148 (1987)).

[0182] III.) 213P1F11-Related Proteins

[0183] Another aspect of the present invention provides 213P1F11-relatedproteins. Specific embodiments of 213P1F11 proteins comprise apolypeptide having all or part of the amino acid sequence of human213P1F11 as shown in FIG. 2 or FIG. 3. Alternatively, embodiments of213P1F11 proteins comprise variant, homolog or analog polypeptides thathave alterations in the amino acid sequence of 213P F11 shown in FIG. 2or FIG. 3.

[0184] In general, naturally occurring allelic variants of human213P1F11 share a high degree of structural identity and homology (e.g.,90% or more homology). Typically, allelic variants of a 213P1F11 proteincontain conservative amino acid substitutions within the 213P1F11sequences described herein or contain a substitution of an amino acidfrom a corresponding position in a homologue of 213P1F11. One class of213P1F11 allelic variants are proteins that share a high degree ofhomology with at least a small region of a particular 213P1F11 aminoacid sequence, but further contain a radical departure from thesequence, such as a non-conservative substitution, truncation, insertionor frame shift. In comparisons of protein sequences, the terms,similarity, identity, and homology each have a distinct meaning asappreciated in the field of genetics. Moreover, orthology and paralogycan be important concepts describing the relationship of members of agiven protein family in one organism to the members of the same familyin other organisms.

[0185] Amino acid abbreviations are provided in Table II. Conservativeamino acid substitutions can frequently be made in a protein withoutaltering either the conformation or the function of the protein.Proteins of the invention can comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,11, 12, 13, 14, 15 conservative substitutions. Such changes includesubstituting any of isoleucine (I), valine (V), and leucine (L) for anyother of these hydrophobic amino acids; aspartic acid (D) for glutamicacid (E) and vice versa; glutamine (O) for asparagine (N) and viceversa; and serine (S) for threonine (T) and vice versa. Othersubstitutions can also be considered conservative, depending on theenvironment of the particular amino acid and its role in thethree-dimensional structure of the protein. For example, glycine (G) andalanine (A) can frequently be interchangeable, as can alanine (A) andvaline (V). Methionine (M), which is relatively hydrophobic, canfrequently be interchanged with leucine and isoleucine, and sometimeswith valine. Lysine (K) and arginine (R) are frequently interchangeablein locations in which the significant feature of the amino acid residueis its charge and the differing pK's of these two amino acid residuesare not significant. Still other changes can be considered“conservative” in particular environments (see, e.g. Table III herein;pages 13-15 “Biochemistry” 2^(nd) ED. Lubert Stryer ed (StanfordUniversity); Henikoff et al., PNAS 1992 Vol 89 10915-10919; Lei et al.,J Biol Chem May 19, 1995; 270(20):11882-6).

[0186] Embodiments of the invention disclosed herein include a widevariety of art-accepted variants or analogs of 213P1F11 proteins such aspolypeptides having amino acid insertions, deletions and substitutions.213P1F11 variants can be made using methods known in the art such assite-directed mutagenesis, alanine scanning, and PCR mutagenesis.Site-directed mutagenesis (Carter et al., Nucl. Acids Res., 13:4331(1986); Zoller et al., Nucl. Acids Res., 10:6487 (1987)), cassettemutagenesis (Wells et al., Gene, 34:315 (1985)), restriction selectionmutagenesis (Wells et al., Philos. Trans. R. Soc. London SerA, 317:415(1986)) or other known techniques can be performed on the cloned DNA toproduce the 213P1F11 variant DNA.

[0187] Scanning amino acid analysis can also be employed to identify oneor more amino acids along a contiguous sequence that is involved in aspecific biological activity such as a protein-protein interaction.Among the preferred scanning amino acids are relatively small, neutralamino acids. Such amino acids include alanine, glycine, serine, andcysteine. Alanine is typically a preferred scanning amino acid amongthis group because it eliminates the side-chain beyond the beta-carbonand is less likely to alter the main-chain conformation of the variant.Alanine is also typically preferred because it is the most common aminoacid. Further, it is frequently found in both buried and exposedpositions (Creighton, The Proteins, (W. H. Freeman & Co., N.Y.);Chothia, J. Mol. Biol., 150:1 (1976)). If alanine substitution does notyield adequate amounts of variant, an isosteric amino acid can be used.

[0188] As defined herein, 213P1F11 variants, analogs or homologs, havethe distinguishing attribute of having at least one epitope that is“cross reactive” with a 213P1F11 protein having an amino acid sequenceof FIG. 3. As used in this sentence, “cross reactive” means that anantibody or T cell that specifically binds to a 213P1F11 variant alsospecifically binds to a 213P1F11 protein having an amino acid sequenceset forth in FIG. 3. A polypeptide ceases to be a variant of a proteinshown in FIG. 3, when it no longer contains any epitope capable of beingrecognized by an antibody or T cell that specifically binds to thestarting 213P1F11 protein. Those skilled in the art understand thatantibodies that recognize proteins bind to epitopes of varying size, anda grouping of the order of about four or five amino acids, contiguous ornot, is regarded as a typical number of amino acids in a minimalepitope. See, e.g., Nair et al., J. Immunol 2000 165(12): 6949-6955;Hebbes et al., Mol Immunol (1989) 26(9):865-73; Schwartz et al., JImmunol (1985) 135(4):2598-608.

[0189] Other classes of 213P1F11-related protein variants share 70%,75%, 80%, 85% or 90% or more similarity with an amino acid sequence ofFIG. 3, or a fragment thereof. Another specific class of 213P1F11protein variants or analogs comprise one or more of the 213P1F11biological motifs described herein or presently known in the art. Thus,encompassed by the present invention are analogs of 213P1F11 fragments(nucleic or amino acid) that have altered functional (e.g. immunogenic)properties relative to the starting fragment. It is to be appreciatedthat motifs now or which become part of the art are to be applied to thenucleic or amino acid sequences of FIG. 2 or FIG. 3.

[0190] As discussed herein, embodiments of the claimed invention includepolypeptides containing less than the full amino acid sequence of a213P1F11 protein shown in FIG. 2 or FIG. 3. For example, representativeembodiments of the invention comprise peptides/proteins having any 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more contiguous amino acids of a213P1F11 protein shown in FIG. 2 or FIG. 3.

[0191] Moreover, representative embodiments of the invention disclosedherein include polypeptides consisting of about amino acid 1 to aboutamino acid 10 of a 213P1F11 protein shown in FIG. 2 or FIG. 3,polypeptides consisting of about amino acid 10 to about amino acid 20 ofa 213P1F11 protein shown in FIG. 2 or FIG. 3, polypeptides consisting ofabout amino acid 20 to about amino acid 30 of a 213P1F11 protein shownin FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 30 toabout amino acid 40 of a 213P1F11 protein shown in FIG. 2 or FIG. 3,polypeptides consisting of about amino acid 40 to about amino acid 50 ofa 213P1F11 protein shown in FIG. 2 or FIG. 3, polypeptides consisting ofabout amino acid 50 to about amino acid 60 of a 213P1F11 protein shownin FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 60 toabout amino acid 70 of a 213P1F11 protein shown in FIG. 2 or FIG. 3,polypeptides consisting of about amino acid 70 to about amino acid 80 ofa 213P1F11 protein shown in FIG. 2 or FIG. 3, polypeptides consisting ofabout amino acid 80 to about amino acid 90 of a 213P1F11 protein shownin FIG. 2 or FIG. 3, polypeptides consisting of about amino acid 90 toabout amino acid 100 of a 213P1F11 protein shown in FIG. 2 or FIG. 3,etc. throughout the entirety of a 213P1F11 amino acid sequence.Moreover, polypeptides consisting of about amino acid 1 (or 20 or 30 or40 etc.) to about amino acid 20, (or 130, or 140 or 150 etc.) of a213P1F11 protein shown in FIG. 2 or FIG. 3 are embodiments of theinvention. It is to be appreciated that the starting and stoppingpositions in this paragraph refer to the specified position as well asthat position plus or minus 5 residues.

[0192] 213P1F11-related proteins are generated using standard peptidesynthesis technology or using chemical cleavage methods well known inthe art. Alternatively, recombinant methods can be used to generatenucleic acid molecules that encode a 213P1F11-related protein. In oneembodiment, nucleic acid molecules provide a means to generate definedfragments of a 213P1F11 protein (or variants, homologs or analogsthereof).

[0193] III.A.) Motif-Bearing Protein Embodiments

[0194] Additional illustrative embodiments of the invention disclosedherein include 213P1F11 polypeptides comprising the amino acid residuesof one or more of the biological motifs contained within a 213P1F11polypeptide sequence set forth in FIG. 2 or FIG. 3. Various motifs areknown in the art, and a protein can be evaluated for the presence ofsuch motifs by a number of publicly available Internet sites (see, e.g.,URL addresses: pfam.wustl.edu/;http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html;psort.ims.u-tokyo.acjp/; www.cbs.dtu.dk/;www.ebi.ac.uk/interpro/scan.html; www.expasy.cb/tools/scnpsit1.html;Epimatrix™ and Epimer™, Brown University,www.brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html; and BIMAS,bimas.dcrt.nih.gov/.).

[0195] Motif bearing subsequences of all 213P1F11 variant proteins areset forth and identified in Tables V-XIX.

[0196] Table XX sets forth several frequently occurring motifs based onpfam searches (see URL address pfam.wustl.edu/). The columns of Table XXlist (1) motif name abbreviation, (2) percent identity found amongst thedifferent member of the motif family, (3) motif name or description and(4) most common function; location information is included if the motifis relevant for location.

[0197] Polypeptides comprising one or more of the 213P1F11 motifsdiscussed above are useful in elucidating the specific characteristicsof a malignant phenotype in view of the observation that the 213P1F11motifs discussed above are associated with growth dysregulation andbecause 213P1F11 is overexpressed in certain cancers (See, e.g., TableI). Casein kinase II, cAMP and camp-dependent protein kinase, andProtein Kinase C, for example, are enzymes known to be associated withthe development of the malignant phenotype (see e.g. Chen et al., LabInvest., 78(2): 165-174 (1998); Gaiddon et al., Endocrinology 136(10):4331-4338 (1995); Hall et al., Nucleic Acids Research 24(6): 1119-1126(1996); Peterziel et al., Oncogene 18(46): 6322-6329 (1999) and O'Brian,Oncol. Rep. 5(2): 305-309 (1998)). Moreover, both glycosylation andmyristoylation are protein modifications also associated with cancer andcancer progression (see e.g. Dennis et al., Biochem. Biophys. Acta1473(1):21-34 (1999); Raju et al., Exp. Cell Res. 235(1): 145-154(1997)). Amidation is another protein modification also associated withcancer and cancer progression (see e.g. Treston et al., J. Natl. CancerInst. Monogr. (13): 169-175 (1992)).

[0198] In another embodiment, proteins of the invention comprise one ormore of the immunoreactive epitopes identified in accordance withart-accepted methods, such as the peptides set forth in Tables V-XIX.CTL epitopes can be determined using specific algorithms to identifypeptides within a 213P1F11 protein that are capable of optimally bindingto specified HLA alleles (e.g., Table IV; Epimatrix™ and Epimer™, BrownUniversity, URLwww.brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html; and BIMAS,URL bimas.dcrt.nih.gov/.) Moreover, processes for identifying peptidesthat have sufficient binding affinity for HLA molecules and which arecorrelated with being immunogenic epitopes, are well known in the art,and are carried out without undue experimentation. In addition,processes for identifying peptides that are immunogenic epitopes, arewell known in the art, and are carried out without undue experimentationeither in vitro or in vivo.

[0199] Also known in the art are principles for creating analogs of suchepitopes in order to modulate immunogenicity. For example, one beginswith an epitope that bears a CTL or HTL motif (see, e.g., the HLA ClassI and HLA Class II motifs/supermotifs of Table IV). The epitope isanaloged by substituting out an amino acid at one of the specifiedpositions, and replacing it with another amino acid specified for thatposition. For example, one can substitute out a deleterious residue infavor of any other residue, such as a preferred residue as defined inTable IV; substitute a less-preferred residue with a preferred residueas defined in Table IV; or substitute an originally-occurring preferredresidue with another preferred residue as defined in Table IV.Substitutions can occur at primary anchor positions or at otherpositions in a peptide; see, e.g., Table IV.

[0200] A variety of references reflect the art regarding theidentification and generation of epitopes in a protein of interest aswell as analogs thereof. See, for example, WO 9733602 to Chesnut et al.;Sette, Immunogenetics 1999 50(3-4): 201-212; Sette et al., J. Immunol.2001 166(2): 1389-1397; Sidney et al., Hum. Immunol. 1997 58(1): 12-20;Kondo et al., Immunogenetics 1997 45(4): 249-258; Sidney et al, J.Immunol. 1996 157(8): 3480-90; and Falk et al., Nature 351: 290-6(1991); Hunt et al, Science 255:1261-3 (1992); Parker et al., J.Immunol. 149:3580-7 (1992); Parker et at, J. Immunol. 152:163-75(1994)); Kast et al, 1994 152(8): 3904-12; Borras-Cuesta et al., Hum.Immunol. 2000 61(3): 266-278; Alexander et al, J. Immunol. 2000 164(3);164(3): 1625-1633; Alexander et al., PMID: 7895164, UI: 95202582;O'Sullivan et al, J. Immunol. 1991 147(8): 2663-2669; Alexander et al.,Immunity 1994 1(9): 751-761 and Alexander et al, Immunol. Res. 199818(2): 79-92.

[0201] Related embodiments of the invention include polypeptidescomprising combinations of the different motifs set forth in Table XXI,and/or, one or more of the predicted CTL epitopes of Tables V-XIX,and/or, one or more of the T cell binding motifs known in the art.Preferred embodiments contain no insertions, deletions or substitutionseither within the motifs or the intervening sequences of thepolypeptides. In addition, embodiments which include a number of eitherN-terminal and/or C-terminal amino acid residues on either side of thesemotifs may be desirable (to, for example, include a greater portion ofthe polypeptide architecture in which the motif is located). Typicallythe number of N-terminal and/or C-terminal amino acid residues on eitherside of a motif is between about 1 to about 100 amino acid residues,preferably 5 to about 50 amino acid residues.

[0202] 213P1F11-related proteins are embodied in many forms, preferablyin isolated form A purified 213P1F11 protein molecule will besubstantially free of other proteins or molecules that impair thebinding of 213P1F11 to antibody, T cell or other ligand. The nature anddegree of isolation and purification will depend on the intended use.Embodiments of a 213P1F11-related proteins include purified213P1F11-related proteins and functional, soluble 213P1F11-relatedproteins. In one embodiment, a functional, soluble 213P1F11 protein orfragment thereof retains the ability to be bound by antibody, T cell orother ligand.

[0203] The invention also provides 213P1F11 proteins comprisingbiologically active fragments of a 213P1F11 amino acid sequence shown inFIG. 2 or FIG. 3. Such proteins exhibit properties of the starting213P1F11 protein, such as the ability to elicit the generation ofantibodies that specifically bind an epitope associated with thestarting 213P1F11 protein; to be bound by such antibodies; to elicit theactivation of HTL or CTL; and/or, to be recognized by HTL or CTL thatalso specifically bind to the starting protein.

[0204] 213P1F11-related polypeptides that contain particularlyinteresting structures can be predicted and/or identified using variousanalytical techniques well known in the art, including, for example, themethods of Chou-Fasman, Gamier-Robson, Kyte-Doolittle, Eisenberg,Karplus-Schultz or Jameson-Wolf analysis, or on the basis ofimmunogenicity. Fragments that contain such structures are particularlyuseful in generating subunit-specific anti-213P1F11 antibodies, or Tcells or in identifying cellular factors that bind to 213P1F11. Forexample, hydrophilicity profiles can be generated, and immunogenicpeptide fragments identified, using the method of Hopp, T. P. and Woods,K. R., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828. Hydropathicityprofiles can be generated, and immunogenic peptide fragments identified,using the method of Kyte, J. and Doolittle, R. F., 1982, J. Mol. Biol.157:105-132. Percent (%) Accessible Residues profiles can be generated,and immunogenic peptide fragments identified, using the method of JaninJ., 1979, Nature 277:491-492. Average Flexibility profiles can begenerated, and immunogenic peptide fragments identified, using themethod of Bhaskaran R., Ponnuswamy P. K., 1988, Int. J. Pept. ProteinRes. 32:242-255. Beta-turn profiles can be generated, and immunogenicpeptide fragments identified, using the method of Deleage, G., Roux B.,1987, Protein Engineering 1:289-294.

[0205] CTL epitopes can be determined using specific algorithms toidentify peptides within a 213P1F11 protein that are capable ofoptimally binding to specified HLA alleles (e.g., by using the SYFPEITHIsite at World Wide Web URL syfpeithi.bmi-heidelberg.com/; the listingsin Table IV(A)-(E); Epimatrix™ and Epimer™, Brown University, URL(www.brown.edu/ResearcI/TB-HIV Lab/epimatrix/epimatrix.html); and BIMAS,URL bimas.dcrt.nih.gov/). Illustrating this, peptide epitopes from213P1F11 that are presented in the context of human MHC Class Imolecules, e.g., HLA-A1, A2, A3, A11, A24, B7 and B35 were predicted(Tables V-XIX). Specifically, the complete amino acid sequence of the213P1F11 protein and relevant portions of other variants, i.e., for HLAClass I predictions 9 flanking redisues on either side of a pointmutation, and for HLA Class II predictions 14 flanking residues oneither side of a point mutation, were entered into the HLA Peptide MotifSearch algorithm found in the Bioinformatics and Molecular AnalysisSection (BIMAS) web site listed above; in addition to the siteSYFPEITHI, at URL syfpeithi.bmi-heidelberg.com/.

[0206] The HLA peptide motif search algorithm was developed by Dr. KenParker based on binding of specific peptide sequences in the groove ofHLA Class I molecules, in particular HLA-A2 (see, e.g., Falk et al.,Nature 351: 290-6 (1991); Hunt et al., Science 255:1261-3 (1992); Parkeret al., J. Immunol. 149:3580-7 (1992); Parker et al., J. Immunol.152:163-75 (1994)). This algorithm allows location and ranking of 8-mer,9-mer (also refered to as “nonamer”), and 10-mer (also refered to as“decamer”) peptides from a complete protein sequence for predictedbinding to HLA-A2 as well as numerous other HLA Class I molecules. ManyHLA class I binding peptides are 8-, 9-, 10 or 11-mers. For example, forClass I HLA-A2, the epitopes preferably contain a leucine (L) ormethionine (M) at position 2 and a valine (V) or leucine (L) at theC-terminus (see, e.g., Parker et al., J. Immunol. 149:3580-7 (1992)).Selected results of 213P1F11 predicted binding peptides are shown inTables V-XIX herein. In Tables V-XIX, the selected candidates, 9-mersand 10-mers, and 15-mers for each family member are shown along withtheir location, the amino acid sequence of each specific peptide, and anestimated binding score. The binding score corresponds to the estimatedhalf time of dissociation of complexes containing the peptide at 37° C.at pH 6.5. Peptides with the highest binding score are predicted to bethe most tightly bound to HLA Class I on the cell surface for thegreatest period of time and thus represent the best immunogenic targetsfor T-cell recognition.

[0207] Actual binding of peptides to an HLA allele can be evaluated bystabilization of HLA expression on the antigen-processing defective cellline T2 (see, e.g., Xue et al., Prostate 30:73-8 (1997) and Peshwa etal., Prostate 36:129-38 (1998)). Immunogenicity of specific peptides canbe evaluated in vitro by stimulation of CD8+ cytotoxic T lymphocytes(CTL) in the presence of antigen presenting cells such as dendriticcells.

[0208] It is to be appreciated that every epitope predicted by the BIMASsite, Epimer™ and Epimatrix™ sites, or specified by the HLA class I orclass II motifs available in the art or which become part of the artsuch as set forth in Table IV (or determined using World Wide Web siteURL syfpeithi.bmi-heidelberg.com/, or BIMAS, bimas.dcrt.nih.gov/) are tobe “applied” to a 213P1F11 protein in accordance with the invention. Asused in this context “applied” means that a 213P1F11 protein isevaluated, e.g., visually or by computer-based patterns finding methods,as appreciated by those of skill in the relevant art. Every subsequenceof a 213P1F11 protein of 8, 9, 10, or 11 amino acid residues that bearsan HLA Class I motif, or a subsequence of 9 or more amino acid residuesthat bear an HLA Class II motif are within the scope of the invention.

[0209] III.B.) Expression of 213P1F11-Related Proteins

[0210] In an embodiment described in the examples that follow, 213P1F11can be conveniently expressed in cells (such as 293T cells) transfectedwith a commercially available expression vector such as a CMV-drivenexpression vector encoding 213P1F11 with a C-terminal 6×His and MYC tag(pcDNA3.1/mycHIS, Invitrogen or Tag5, GenHunter Corporation, NashvilleTenn.). The Tag5 vector provides an IgGK secretion signal that can beused to facilitate the production of a secreted 213P1F11 protein intransfected cells. The secreted HIS-tagged 213P1F11 in the culture mediacan be purified, e.g., using a nickel column using standard techniques.

[0211] III.C.) Modifications of 213P1F11-Related Proteins

[0212] Modifications of 213P1F11-related proteins such as covalentmodifications are included within the scope of this invention. One typeof covalent modification includes reacting targeted amino acid residuesof a 213P1F11 polypeptide with an organic derivatizing agent that iscapable of reacting with selected side chains or the N- or C-terminalresidues of a 213P1F11 protein. Another type of covalent modification ofa 213P1F11 polypeptide included within the scope of this inventioncomprises altering the native glycosylation pattern of a protein of theinvention. Another type of covalent modification of 213P1F11 compriseslinking a 213P1F11 polypeptide to one of a variety of nonproteinaceouspolymers, e.g., polyethylene glycol (PEG), polypropylene glycol, orpolyoxyalkylenes, in the manner set forth in U.S. Pat. Nos. 4,640,835;4,496,689; 4,301,144; 4,670,417; 4,791,192 or 4,179,337.

[0213] The 213P1F11-related proteins of the present invention can alsobe modified to form a chimeric molecule comprising 213P1F11 fused toanother, heterologous polypeptide or amino acid sequence. Such achimeric molecule can be synthesized chemically or recombinantly. Achimeric molecule can have a protein of the invention fused to anothertumor-associated antigen or fragment thereof. Alternatively, a proteinin accordance with the invention can comprise a fusion of fragments of a213P1F11 sequence (amino or nucleic acid) such that a molecule iscreated that is not, through its length, directly homologous to theamino or nucleic acid sequences shown in FIG. 2 or FIG. 3. Such achimeric molecule can comprise multiples of the same subsequence of213P1F11. A chimeric molecule can comprise a fusion of a213P1F11-related protein with a polyhistidine epitope tag, whichprovides an epitope to which immobilized nickel can selectively bind,with cytokines or with growth factors. The epitope tag is generallyplaced at the amino- or carboxyl-terminus of a 213P1F11 protein. In analternative embodiment, the chimeric molecule can comprise a fusion of a213P1F11-related protein with an immunoglobulin or a particular regionof an immunoglobulin. For a bivalent form of the chimeric molecule (alsoreferred to as an “immunoadlesin”), such a fusion could be to the Fcregion of an IgG molecule. The Ig fusions preferably include thesubstitution of a soluble (transmembrane domain deleted or inactivated)form of a 213P1F11 polypeptide in place of at least one variable regionwithin an Ig molecule. In a preferred embodiment, the immunoglobulinfusion includes the hinge, CH2 and CH3, or the hinge, CH1, CH2 and CH3regions of an IgG1 molecule. For the production of immunoglobulinfusions see, e.g., U.S. Pat. No. 5,428,130 issued Jun. 27, 1995.

[0214] III.D.) Uses of 213P1F11-Related Proteins

[0215] The proteins of the invention have a number of different specificuses. As 213P1F11 is highly expressed in prostate and other cancers,213P1F11-related proteins are used in methods that assess the status of213P1F11 gene products in normal versus cancerous tissues, therebyelucidating the malignant phenotype. Typically, polypeptides fromspecific regions of a 213P1F11 protein are used to assess the presenceof perturbations (such as deletions, insertions, point mutations etc.)in those regions (such as regions containing one or more motifs).Exemplary assays utilize antibodies or T cells targeting213P1F11-related proteins comprising the amino acid residues of one ormore of the biological motifs contained within a 213P1F11 polypeptidesequence in order to evaluate the characteristics of this region innormal versus cancerous tissues or to elicit an immune response to theepitope. Alternatively, 213P1F11-related proteins that contain the aminoacid residues of one or more of the biological motifs in a 213P1F11protein are used to screen for factors that interact with that region of213P1F11.

[0216] 213P1F11 protein fragments/subsequences are particularly usefulin generating and characterizing domain-specific antibodies (e.g.,antibodies recognizing an extracellular or intracellular epitope of a213P1F11 protein), for identifying agents or cellular factors that bindto 213P1F11 or a particular structural domain thereof, and in varioustherapeutic and diagnostic contexts, including but not limited todiagnostic assays, cancer vaccines and methods of preparing suchvaccines.

[0217] Proteins encoded by the 213P1F11 genes, or by analogs, homologsor fragments thereof, have a variety of uses, including but not limitedto generating antibodies and in methods for identifying ligands andother agents and cellular constituents that bind to a 213P1F11 geneproduct. Antibodies raised against a 213P1F11 protein or fragmentthereof are useful in diagnostic and prognostic assays, and imagingmethodologies in the management of human cancers characterized byexpression of 213P1F11 protein, such as those listed in Table I. Suchantibodies can be expressed intracellularly and used in methods oftreating patients with such cancers. 213P1F11-related nucleic acids orproteins are also used in generating HTL or CTL responses.

[0218] Various immunological assays useful for the detection of 213P1F11proteins are used, including but not limited to various types ofradioimmunoassays, enzyme-linked immunosorbent assays (ELISA),enzyme-linked immunofluorescent assays (ELIFA), immunocytochemicalmethods, and the like. Antibodies can be labeled and used asimmunological imaging reagents capable of detecting 213P1F11-expressingcells (e.g., in radioscintigrapbic imaging methods). 213P1F11 proteinsare also particularly useful in generating cancer vaccines, as furtherdescribed herein.

[0219] IV.) 213P1F11 Antibodies

[0220] Another aspect of the invention provides antibodies that bind to213P1F11-related proteins. Preferred antibodies specifically bind to a213P1F11-related protein and do not bind (or bind weakly) to peptides orproteins that are not 213P1F11-related proteins. For example, antibodiesthat bind 213P1F11 can bind 213P1F11-related proteins such as thehomologs or analogs thereof.

[0221] 213P1F11 antibodies of the invention are particularly useful incancer (see, e.g., Table I) diagnostic and prognostic assays, andimaging methodologies. Similarly, such antibodies are useful in thetreatment, diagnosis, and/or prognosis of other cancers, to the extent213P1F11 is also expressed or overexpressed in these other cancers.Moreover, intracellularly expressed antibodies (e.g., single chainantibodies) are therapeutically useful in treating cancers in which theexpression of 213P1F11 is involved, such as advanced or metastaticprostate cancers.

[0222] The invention also provides various immunological assays usefulfor the detection and quantification of 213P1F11 and mutant213P1F11-related proteins. Such assays can comprise one or more 213P1F11antibodies capable of recognizing and binding a 213P1F11-relatedprotein, as appropriate. These assays are performed within variousimmunological assay formats well known in the art, including but notlimited to various types of radioimmunoassays, enzyme-linkedimmunosorbent assays (ELISA), enzyme-linked immunofluorescent assays(ELIFA), and the like.

[0223] Immunological non-antibody assays of the invention also compriseT cell inmmunogenicity assays (inhibitory or stimulatory) as well asmajor histocompatibility complex (MHC) binding assays.

[0224] In addition, immunological imaging methods capable of detectingprostate cancer and other cancers expressing 213P1F11 are also providedby the invention, including but not limited to radioscintigraphicimaging methods using labeled 213P1F11 antibodies. Such assays areclinically useful in the detection, monitoring, and prognosis of213P1F11 expressing cancers such as prostate cancer.

[0225] 213P1F11 antibodies are also used in methods for purifying a213P1F11-related protein and for isolating 213P1F11 homologues andrelated molecules. For example, a method of purifying a 213P1F11-relatedprotein comprises incubating a 213P1F11 antibody, which has been coupledto a solid matrix, with a lysate or other solution containing a213P1F11-related protein under conditions that permit the 213P1F11antibody to bind to the 213P1F11-related protein; washing the solidmatrix to eliminate impurities; and eluting the 213P1F11-related proteinfrom the coupled antibody. Other uses of 213P1F11 antibodies inaccordance with the invention include generating anti-idiotypicantibodies that mimic a 213P1F11 protein.

[0226] Various methods for the preparation of antibodies are well knownin the art. For example, antibodies can be prepared by immunizing asuitable mammalian host using a 213P1F11-related protein, peptide, orfragment, in isolated or immunoconjugated form (Antibodies: A LaboratoryManual, CSH Press, Eds., Harlow, and Lane (1988); Harlow, Antibodies,Cold Spring Harbor Press, NY (1989)). In addition, fusion proteins of213P1F11 can also be used, such as a 213P1F11 GST-fusion protein. In aparticular embodiment, a GST fusion protein comprising all or most ofthe amino acid sequence of FIG. 2 or FIG. 3 is produced, then used as animmunogen to generate appropriate antibodies. In another embodiment, a213P1F11-related protein is synthesized and used as an immunogen.

[0227] In addition, naked DNA immunization techniques known in the artare used (with or without purified 213P1F11-related protein or 213P1F11expressing cells) to generate an immune response to the encodedimmunogen (for review, see Donnelly et al., 1997, Ann. Rev. Immunol. 15:617-648).

[0228] The amino acid sequence of a 213P1F11 protein as shown in FIG. 2or FIG. 3 can be analyzed to select specific regions of the 213P1F11protein for generating antibodies. For example, hydrophobicity andhydrophilicity analyses of a 213P1F11 amino acid sequence are used toidentify hydrophilic regions in the 213P1F11 structure. Regions of a213P1F11 protein that show immunogenic structure, as well as otherregions and domains, can readily be identified using various othermethods known in the art, such as Chou-Fasman, Gamier-Robson,Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf analysis.Hydrophilicity profiles can be generated using the method of Hopp, T. P.and Woods, K. R., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828.Hydropathicity profiles can be generated using the method of Kyte, J.and Doolittle, R. F., 1982, J. Mol. Biol. 157:105-132. Percent (%)Accessible Residues profiles can be generated using the method of JaninJ., 1979, Nature 277:491-492. Average Flexibility profiles can begenerated using the method of Bhaskaran R., Ponnuswamy P. K., 1988, Int.J. Pept. Protein Res. 32:242-255. Beta-turn profiles can be generatedusing the method of Deleage, G., Roux B., 1987, Protein Engineering1:289-294. Thus, each region identified by any of these programs ormethods is within the scope of the present invention. Methods for thegeneration of 213P1F11 antibodies are further illustrated by way of theexamples provided herein. Methods for preparing a protein or polypeptidefor use as an immunogen are well known in the art. Also well known inthe art are methods for preparing immunogenic conjugates of a proteinwith a carrier, such as BSA, KLH or other carrier protein. In somecircumstances, direct conjugation using, for example, carbodiimidereagents are used; in other instances linking reagents such as thosesupplied by Pierce Chemical Co., Rockford, Ill., are effective.Administration of a 213P1F11 immunogen is often conducted by injectionover a suitable time period and with use of a suitable adjuvant, as isunderstood in the art. During the immunization schedule, titers ofantibodies can be taken to determine adequacy of antibody formation.

[0229] 213P1F11 monoclonal antibodies can be produced by various meanswell known in the art. For example, immortalized cell lines that secretea desired monoclonal antibody are prepared using the standard hybridomatechnology of Kohler and Milstein or modifications that immortalizeantibody-producing B cells, as is generally known. Immortalized celllines that secrete the desired antibodies are screened by immunoassay inwhich the antigen is a 213P1F11-related protein. When the appropriateimmortalized cell culture is identified, the cells can be expanded andantibodies produced either from in vitro cultures or from ascites fluid.

[0230] The antibodies or fragments of the invention can also beproduced, by recombinant means. Regions that bind specifically to thedesired regions of a 213P1F11 protein can also be produced in thecontext of chimeric or complementarity determining region (CDR) graftedantibodies of multiple species origin. Humanized or human 213P1F11antibodies can also be produced, and are preferred for use intherapeutic contexts. Methods for humanizing murine and other non-humanantibodies, by substituting one or more of the non-human antibody CDRsfor corresponding human antibody sequences, are well known (see forexample, Jones et al., 1986, Nature 321: 522-525; Riechmann et al.,1988, Nature 332: 323-327; Verhoeyen et al., 1988, Science 239:1534-1536). See also, Carter et al., 1993, Proc. Natl. Acad. Sci. USA89: 4285 and Simns et al., 1993, J. Immunol. 151: 2296.

[0231] Methods for producing fully human monoclonal antibodies includephage display and transgenic methods (for review, see Vaughan et al.,1998, Nature Biotechnology 16: 535-539). Fully human 213P1F11 monoclonalantibodies can be generated using cloning technologies employing largehuman Ig gene combinatorial libraries (i.e., phage display) (Griffithsand Hoogenboom, Building an in vitro immune system: human antibodiesfrom phage display libraries. In: Protein Engineering of AntibodyMolecules for Prophylactic and Therapeutic Applications in Man, Clark,M. (Ed.), Nottingham Academic, pp 45-64 (1993); Burton and Barbas, HumanAntibodies from combinatorial libraries. Id., pp 65-82). Fully human213P1F11 monoclonal antibodies can also be produced using transgenicmice engineered to contain human immunoglobulin gene loci as describedin PCT Patent Application WO98/24893, Kucherlapati and Jakobovits etal., published Dec. 3, 1997 (see also, Jakobovits, 1998, Exp. Opin.Invest. Drugs 7(4): 607-614; U.S. Pat. No. 6,162,963 issued Dec. 19,2000; U.S. Pat. No. 6,150,584 issued Nov. 12, 2000; and, U.S. Pat. No.6,11,4598 issued Sep. 5, 2000). This method avoids the in vitromanipulation required with phage display technology and efficientlyproduces high affinity authentic human antibodies.

[0232] Reactivity of 213P1F11 antibodies with a 213P1F11-related proteincan be established by a number of well known means, including Westernblot, immunoprecipitation, ELISA, and FACS analyses using, asappropriate, 213P1F11-related proteins, 213P1F11-expressing cells orextracts thereof. A 213P1F11 antibody or fragment thereof can be labeledwith a detectable marker or conjugated to a second molecule. Suitabledetectable markers include, but are not limited to, a radioisotope, afluorescent compound, a bioluminescent compound, chemiluminescentcompound, a metal chelator or an enzyme. Further, bi-specific antibodiesspecific for two or more 213P1F11 epitopes are generated using methodsgenerally known in the art. Homodimeric antibodies can also be generatedby cross-linking techniques known in the art (e.g., Wolff et al., CancerRes. 53: 2560-2565).

[0233] V.) 213P1F11 Cellular Immune Responses

[0234] The mechanism by which T cells recognize antigens has beendelineated. Efficacious peptide epitope vaccine compositions of theinvention induce a therapeutic or prophylactic immune responses in verybroad segments of the world-wide population. For an understanding of thevalue and efficacy of compositions of the invention that induce cellularimmune responses, a brief review of immunology-related technology isprovided.

[0235] A complex of an HLA molecule and a peptidic antigen acts as theligand recognized by HLA-restricted T cells (Buus, S. et al., Cell47:1071, 1986; Babbitt, B. P. et al., Nature 317:359, 1985; Townsend, A.and Bodimer, H., Annu. Rev. Immunol. 7:601, 1989; Germain, R. N., Annu.Rev. Immunol. 11:403, 1993). Through the study of single amino acidsubstituted antigen analogs and the sequencing of endogenously bound,naturally processed peptides, critical residues that correspond tomotifs required for specific binding to HLA antigen molecules have beenidentified and are set forth in Table IV (see also, e.g., Southwood, etal., J. Immunol. 160:3363, 1998; Rammensee, et al., Immunogenetics41:178, 1995; Rammensee et al., SYFPEITHI, access via World Wide Web atURL syfpeithi.bmi-heidelberg.com/; Sette, A. and Sidney, J. Curr. Opin.Immunol. 10:478, 1998; Engelhard, V. H., Curr. Opin. Immunol. 6:13,1994; Sette, A. and Grey, H. M., Curr. Opin. Immunol. 4:79, 1992;Sinigaglia, F. and Hammer, J. Curr. Biol. 6:52, 1994; Ruppert et al.,Cell 74:929-937, 1993; Kondo et al., J. Immunol. 155:4307-4312, 1995;Sidney et al., J. Immunol. 157:3480-3490, 1996; Sidney et al., HumanImmunol. 45:79-93, 1996; Sette, A. and Sidney, J. ImmunogeneticsNovember 1999; 50(3-4):201-12, Review).

[0236] Furthermore, x-ray crystallographic analyses of HLA-peptidecomplexes have revealed pockets within the peptide binding cleft/grooveof HLA molecules which accommodate, in an allele-specific mode, residuesborne by peptide ligands; these residues in turn determine the HLAbinding capacity of the peptides in which they are present. (See, e.g.,Madden, D. R. Annu. Rev. Immunol. 13:587, 1995; Smith, et al., Immunity4:203, 1996; Fremont et al., Immunity 8:305, 1998; Stem et al.,Structure 2:245, 1994; Jones, E. Y. Curr. Opin. Immunol. 9:75, 1997;Brown, J. H. et al., Nature 364:33, 1993; Guo, H. C. et al., Proc. Natl.Acad. Sci. USA 90:8053, 1993; Guo, H. C. et al., Nature 360:364, 1992;Silver, M. L. et al., Nature 360:367, 1992; Matsumura, M. et al.,Science 257:927, 1992; Madden et al., Cell 70:1035, 1992; Fremont, D. H.et al., Science 257:919, 1992; Saper, M. A., Bjorkman, P. J. and Wiley,D. C., J. Mol. Biol. 219:277, 1991.)

[0237] Accordingly, the definition of class I and class IIallele-specific HLA binding motifs, or class I or class II supermotifsallows identification of regions within a protein that are correlatedwith binding to particular HLA antigen(s).

[0238] Thus, by a process of HLA motif identification, candidates forepitope-based vaccines have been identified; such candidates can befurther evaluated by HLA-peptide binding assays to determine bindingaffinity and/or the time period of association of the epitope and itscorresponding HLA molecule. Additional confirmatory work can beperformed to select, amongst these vaccine candidates, epitopes withpreferred characteristics in terms of population coverage, and/orimmunogenicity.

[0239] Various strategies can be utilized to evaluate cellularimmunogenicity, including:

[0240] 1) Evaluation of primary T cell cultures from normal individuals(see, e.g., Wentworth, P. A. et al., Mol. Immunol. 32:603, 1995; Celis,E. et al., Proc. Natl. Acad. Sci. USA 91:2105, 1994; Tsai, V. et al., J.Immunol. 158:1796, 1997; Kawashima, I. et al., Human Immunol. 59:1,1998). This procedure involves the stimulation of peripheral bloodlymphocytes (PBL) from normal subjects with a test peptide in thepresence of antigen presenting cells in vitro over a period of severalweeks. T cells specific for the peptide become activated during thistime and are detected using, e.g., a lymphokine- or ⁵¹Cr-release assayinvolving peptide sensitized target cells.

[0241] 2) Immunization of HLA transgenic mice (see, e.g., Wentworth, P.A. et al., J. Immunol. 26:97, 1996; Wentworth, P. A. et al., Int.Immunol. 8:651, 1996; Alexander, J. et al., J. Immunol. 159:4753, 1997).For example, in such methods peptides in incomplete Freund's adjuvantare administered subcutaneously to HLA transgenic mice. Several weeksfollowing immunization, splenocytes are removed and cultured in vitro inthe presence of test peptide for approximately one week.Peptide-specific T cells are detected using, e.g., a ⁵¹Cr-release assayinvolving peptide sensitized target cells and target cells expressingendogenously generated antigen.

[0242] 3) Demonstration of recall T cell responses from immuneindividuals who have been either effectively vaccinated and/or fromchronically ill patients (see, e.g., Rehermann, B. et al, J. Exp. Med.181:1047, 1995; Doolan, D. L. et al., Immunity 7:97, 1997; Bertoni, R.et al., J. Clin. Invest. 100:503, 1997; Threlkeld, S. C. et al., J.Immunol. 159:1648, 1997; Diepolder, H. M. et al., J. Virol. 71:6011,1997). Accordingly, recall responses are detected by culturing PBL fromsubjects that have been exposed to the antigen due to disease and thushave generated an immune response “naturally”, or from patients who werevaccinated against the antigen. PBL from subjects are cultured in vitrofor 1-2 weeks in the presence of test peptide plus antigen presentingcells (APC) to allow activation of “memory” T cells, as compared to“naive” T cells. At the end of the culture period, T cell activity isdetected using assays including ⁵¹Cr release involvingpeptide-sensitized targets, T cell proliferation, or lymphokine release.

[0243] VI.) 213P1F11 Transgenic Animals

[0244] Nucleic acids that encode a 213P1F11-related protein can also beused to generate either transgenic animals or “knock out” animals that,in turn, are useful in the development and screening of therapeuticallyuseful reagents. In accordance with established techniques, cDNAencoding 213P1F11 can be used to clone genomic DNA that encodes213P1F11. The cloned genomic sequences can then be used to generatetransgenic animals containing cells that express DNA that encode213P1F11. Methods for generating transgenic animals, particularlyanimals such as mice or rats, have become conventional in the art andare described, for example, in U.S. Pat. No. 4,736,866 issued Apr. 12,1988, and U.S. Pat. No. 4,870,009 issued Sep. 26, 1989. Typically,particular cells would be targeted for 213P1F11 transgene incorporationwith tissue-specific enhancers.

[0245] Transgenic animals that include a copy of a transgene encoding213P1F11 can be used to examine the effect of increased expression ofDNA that encodes 213P1F11. Such animals can be used as tester animalsfor reagents thought to confer protection from, for example,pathological conditions associated with its overexpression. Inaccordance with this aspect of the invention, an animal is treated witha reagent and a reduced incidence of a pathological condition, comparedto untreated animals that bear the transgene, would indicate a potentialtherapeutic intervention for the pathological condition.

[0246] Alternatively, non-human homologues of 213P1F11 can be used toconstruct a 213P1F11 “knock out” animal that has a defective or alteredgene encoding 213P1F11 as a result of homologous recombination betweenthe endogenous gene encoding 213P1F11 and altered genomic DNA encoding213P1F11 introduced into an embryonic cell of the animal. For example,cDNA that encodes 213P F11 can be used to clone genomic DNA encoding213P1F11 in accordance with established techniques. A portion of thegenomic DNA encoding 213P1F11 can be deleted or replaced with anothergene, such as a gene encoding a selectable marker that can be used tomonitor integration. Typically, several kilobases of unaltered flankingDNA (both at the 5′ and 3′ ends) are included in the vector (see, e.g.,Thomas and Capecchi, Cell, 51:503 (1987) for a description of homologousrecombination vectors). The vector is introduced into an embryonic stemcell line (e.g., by electroporation) and cells in which the introducedDNA has homologously recombined with the endogenous DNA are selected(see, e.g., Li et al, Cell, 69:915 (1992)). The selected cells are theninjected into a blastocyst of an animal (e.g., a mouse or rat) to formaggregation chimeras (see, e.g., Bradley, in Teratocarcinomas andEmbryonic Stem Cells: A Practical Approach, E. J. Robertson, ed. (IRL,Oxford, 1987), pp. 113-152). A chimeric embryo can then be implantedinto a suitable pseudopregnant female foster animal, and the embryobrought to term to create a “knock out” animal. Progeny harboring thehomologously recombined DNA in their germ cells can be identified bystandard techniques and used to breed animals in which all cells of theanimal contain the homologously recombined DNA. Knock out animals can becharacterized, for example, for their ability to defend against certainpathological conditions or for their development of pathologicalconditions due to absence of a 213P1F11 polypeptide.

[0247] VII.) Methods for the Detection of 213P1F11

[0248] Another aspect of the present invention relates to methods fordetecting 213P1F11 polynucleotides and 213P1F11-related proteins, aswell as methods for identifying a cell that expresses 213P1F11. Theexpression profile of 213P1F11 makes it a diagnostic marker formetastasized disease. Accordingly, the status of 213P1F11 gene productsprovides information useful for predicting a variety of factorsincluding susceptibility to advanced stage disease, rate of progression,and/or tumor aggressiveness. As discussed in detail herein, the statusof 213P1F11 gene products in patient samples can be analyzed by avariety protocols that are well known in the art includingimmunohistochemical analysis, the variety of Northern blottingtechniques including in situ hybridization, RT-PCR analysis (for exampleon laser capture micro-dissected samples), Western blot analysis andtissue array analysis.

[0249] More particularly, the invention provides assays for thedetection of 213P1F11 polynucleotides in a biological sample, such asserum, bone, prostate, and other tissues, urine, semen, cellpreparations, and the like. Detectable 213P1F11 polynucleotides include,for example, a 213P1F11 gene or fragment thereof, 213P1F11 mRNA,alternative splice variant 213P1F11 mRNAs, and recombinant DNA or RNAmolecules that contain a 213P1F11 polynucleotide. A number of methodsfor amplifying and/or detecting the presence of 213P1F11 polynucleotidesare well known in the art and can be employed in the practice of thisaspect of the invention.

[0250] In one embodiment, a method for detecting a 213P1F11 mRNA in abiological sample comprises producing cDNA from the sample by reversetranscription using at least one primer; amplifying the cDNA so producedusing a 213P1F11 polynucleotides as sense and antisense primers toamplify 213P1F11 cDNAs therein; and detecting the presence of theamplified 213P1F11 cDNA. Optionally, the sequence of the amplified213P1F11 cDNA can be determined.

[0251] In another embodiment, a method of detecting a 213P1F11 gene in abiological sample comprises first isolating genomic DNA from the sample;amplifying the isolated genomic DNA using 213P1F11 polynucleotides assense and antisense primers; and detecting the presence of the amplified213P1F11 gene. Any number of appropriate sense and antisense probecombinations can be designed from a 213P1F11 nucleotide sequence (see,e.g., FIG. 2) and used for this purpose.

[0252] The invention also provides assays for detecting the presence ofa 213P1F11 protein in a tissue or other biological sample such as serum,semen, bone, prostate, urine, cell preparations, and the like. Methodsfor detecting a 213P1F11-related protein are also well known andinclude, for example, immunoprecipitation, immunohistochemical analysis,Western blot analysis, molecular binding assays, ELISA, ELIFA and thelike. For example, a method of detecting the presence of a213P1F11-related protein in a biological sample comprises firstcontacting the sample with a 213P1F11 antibody, a 213P1F11-reactivefragment thereof, or a recombinant protein containing an antigen bindingregion of a 213P1F11 antibody; and then detecting the binding of213P1F11-related protein in the sample.

[0253] Methods for identifying a cell that expresses 213P1F11 are alsowithin the scope of the invention. In one embodiment, an assay foridentifying a cell that expresses a 213P1F11 gene comprises detectingthe presence of 213P1F11 mRNA in the cell. Methods for the detection ofparticular mRNAs in cells are well known and include, for example,hybridization assays using complementary DNA probes (such as in situhybridization using labeled 213P1F11 riboprobes, Northern blot andrelated techniques) and various nucleic acid amplification assays (suchas RT-PCR using complementary primers specific for 213P1F11, and otheramplification type detection methods, such as, for example, branchedDNA, SISBA, TMA and the like). Alternatively, an assay for identifying acell that expresses a 213P1F11 gene comprises detecting the presence of213P1F11-related protein in the cell or secreted by the cell. Variousmethods for the detection of proteins are well known in the art and areemployed for the detection of 213P1F11-related proteins and cells thatexpress 213P1F11-related proteins.

[0254] 213P1F11 expression analysis is also useful as a tool foridentifying and evaluating agents that modulate 213P1F11 geneexpression. For example, 213P1F11 expression is significantlyupregulated in prostate cancer, and is expressed in cancers of thetissues listed in Table I. Identification of a molecule or biologicalagent that inhibits 213P1F11 expression or over-expression in cancercells is of therapeutic value. For example, such an agent can beidentified by using a screen that quantifies 213P1F11 expression byRT-PCR, nucleic acid hybridization or antibody binding.

[0255] VIII.) Methods for Monitoring the Status of 213P1F11-relatedGenes and Their Products

[0256] Oncogenesis is known to be a multistep process where cellulargrowth becomes progressively dysregulated and cells progress from anormal physiological state to precancerous and then cancerous states(see, e.g., Alers et al., Lab Invest. 77(5): 437-438 (1997) and Isaacset al., Cancer Surv. 23: 19-32 (1995)). In this context, examining abiological sample for evidence of dysregulated cell growth (such asaberrant 213P1F11 expression in cancers) allows for early detection ofsuch aberrant physiology, before a pathologic state such as cancer hasprogressed to a stage that therapeutic options are more limited and orthe prognosis is worse. In such examinations, the status of 213P1F11 ina biological sample of interest can be compared, for example, to thestatus of 213P1F11 in a corresponding normal sample (e.g. a sample fromthat individual or alternatively another individual that is not affectedby a pathology). An alteration in the status of 213P1F11 in thebiological sample (as compared to the normal sample) provides evidenceof dysregulated cellular growth. In addition to using a biologicalsample that is not affected by a pathology as a normal sample, one canalso use a predetermined normative value such as a predetermined normallevel of mRNA expression (see, e.g., Grever et al., J. Comp. Neurol.Dec. 9, 1996; 376(2): 306-14 and U.S. Pat. No. 5,837,501) to compare213P1F11 status in a sample.

[0257] The term “status” in this context is used according to its artaccepted meaning and refers to the condition or state of a gene and itsproducts. Typically, skilled artisans use a number of parameters toevaluate the condition or state of a gene and its products. Theseinclude, but are not limited to the location of expressed gene products(including the location of 213P1F11 expressing cells) as well as thelevel, and biological activity of expressed gene products (such as213P1F11 mRNA, polynucleotides and polypeptides). Typically, analteration in the status of 213P1F11 comprises a change in the locationof 213P1F11 and/or 213P1F11 expressing cells and/or an increase in213P1F11 mRNA and/or protein expression.

[0258] 213P1F11 status in a sample can be analyzed by a number of meanswell known in the art, including without limitation, immunohistochemicalanalysis, in situ hybridization, RT-PCR analysis on laser capturemicro-dissected samples, Western blot analysis, and tissue arrayanalysis. Typical protocols for evaluating the status of a 213P1F11 geneand gene products are found, for example in Ausubel et al. eds., 1995,Current Protocols In Molecular Biology, Units 2 (Northern Blotting), 4(Southern Blotting), 15 (Immunoblotting) and 18 (PCR Analysis). Thus,the status of 213P1F11 in a biological sample is evaluated by variousmethods utilized by skilled artisans including, but not limited togenomic Southern analysis (to examine, for example perturbations in a213P1F11 gene), Northern analysis and/or PCR analysis of 213P1F11 mRNA(to examine, for example alterations in the polynucleotide sequences orexpression levels of 213P1F11 mRNAs), and, Western and/orimmunohistochemical analysis (to examine, for example alterations inpolypeptide sequences, alterations in polypeptide localization within asample, alterations in expression levels of 213P1F11 proteins and/orassociations of 213P1F11 proteins with polypeptide binding partners).Detectable 213P1F11 polynucleotides include, for example, a 213P1F11gene or fragment thereof, 213P1F11 mRNA, alternative splice variants,213P1F11 mRNAs, and recombinant DNA or RNA molecules containing a213P1F11 polynucleotide.

[0259] The expression profile of 213P1F11 makes it a diagnostic markerfor local and/or metastasized disease, and provides information on thegrowth or oncogenic potential of a biological sample. In particular, thestatus of 213P1F11 provides information useful for predictingsusceptibility to particular disease stages, progression, and/or tumoraggressiveness. The invention provides methods and assays fordetermining 213P1F11 status and diagnosing cancers that express213P1F11, such as cancers of the tissues listed in Table I. For example,because 213P1F11 mRNA is so highly expressed in prostate and othercancers relative to normal prostate tissue, assays that evaluate thelevels of 213P1F11 mRNA transcripts or proteins in a biological samplecan be used to diagnose a disease associated with 213P1F11dysregulation, and can provide prognostic information useful in definingappropriate therapeutic options.

[0260] The expression status of 213P1F11 provides information includingthe presence, stage and location of dysplastic, precancerous andcancerous cells, predicting susceptibility to various stages of disease,and/or for gauging tumor aggressiveness. Moreover, the expressionprofile makes it useful as an imaging reagent for metastasized disease.Consequently, an aspect of the invention is directed to the variousmolecular prognostic and diagnostic methods for examining the status of213P1F11 in biological samples such as those from individuals sufferingfrom, or suspected of suffering from a pathology characterized bydysregulated cellular growth, such as cancer.

[0261] As described above, the status of 213P1F11 in a biological samplecan be examined by a number of well-known procedures in the art. Forexample, the status of 213P1F11 in a biological sample taken from aspecific location in the body can be examined by evaluating the samplefor the presence or absence of 213P1F11 expressing cells (e.g. thosethat express 213P1F11 mRNAs or proteins). This examination can provideevidence of dysregulated cellular growth, for example, when213P1F11-expressing cells are found in a biological sample that does notnormally contain such cells (such as a lymph node), because suchalterations in the status of 213P1F11 in a biological sample are oftenassociated with dysregulated cellular growth. Specifically, oneindicator of dysregulated cellular growth is the metastases of cancercells from an organ of origin (such as the prostate) to a different areaof the body (such as a lymph node). In this context, evidence ofdysregulated cellular growth is important for example because occultlymph node metastases can be detected in a substantial proportion ofpatients with prostate cancer, and such metastases are associated withknown predictors of disease progression (see, e.g., Murphy et al.,Prostate 42(4): 315-317 (2000);Su et al., Semin. Surg. Oncol. 18(1):17-28 (2000) and Freeman et al., J Urol August 1995 154(2 Pt 1):474-8).

[0262] In one aspect, the invention provides methods for monitoring213P1F11 gene products by determining the status of 213P1F11 geneproducts expressed by cells from an individual suspected of having adisease associated with dysregulated cell growth (such as hyperplasia orcancer) and then comparing the status so determined to the status of213P1F11 gene products in a corresponding normal sample. The presence ofaberrant 213P1F11 gene products in the test sample relative to thenormal sample provides an indication of the presence of dysregulatedcell growth within the cells of the individual.

[0263] In another aspect, the invention provides assays useful indetermining the presence of cancer in an individual, comprisingdetecting a significant increase in 213P1F11 mRNA or protein expressionin a test cell or tissue sample relative to expression levels in thecorresponding normal cell or tissue. The presence of 213P1F11 mRNA can,for example, be evaluated in tissues including but not limited to thoselisted in Table I. The presence of significant 213P1F11 expression inany of these tissues is useful to indicate the emergence, presenceand/or severity of a cancer, since the corresponding normal tissues donot express 213P1F11 mRNA or express it at lower levels.

[0264] In a related embodiment, 213P1F11 status is determined at theprotein level rather than at the nucleic acid level. For example, such amethod comprises determining the level of 213P1F11 protein expressed bycells in a test tissue sample and comparing the level so determined tothe level of 213P1F11 expressed in a corresponding normal sample. In oneembodiment, the presence of 213P1F11 protein is evaluated, for example,using immunohistochemical methods. 213P1F11 antibodies or bindingpartners capable of detecting 213P1F11 protein expression are used in avariety of assay formats well known in the art for this purpose.

[0265] In a further embodiment, one can evaluate the status of 213P1F11nucleotide and amino acid sequences in a biological sample in order toidentify perturbations in the structure of these molecules. Theseperturbations can include insertions, deletions, substitutions and thelike. Such evaluations are useful because perturbations in thenucleotide and amino acid sequences are observed in a large number ofproteins associated with a growth dysregulated phenotype (see, e.g.,Marrogi et al., 1999, J. Cutan. Pathol. 26(8):369-378). For example, amutation in the sequence of 213P1F11 may be indicative of the presenceor promotion of a tumor. Such assays therefore have diagnostic andpredictive value where a mutation in 213P1F11 indicates a potential lossof function or increase in tumor growth.

[0266] A wide variety of assays for observing perturbations innucleotide and amino acid sequences are well known in the art. Forexample, the size and structure of nucleic acid or amino acid sequencesof 213P1F11 gene products are observed by the Northern, Southern,Western, PCR and DNA sequencing protocols discussed herein. In addition,other methods for observing perturbations in nucleotide and amino acidsequences such as single strand conformation polymorphism analysis arewell known in the art (see, e.g., U.S. Pat. No. 5,382,510 issued Sep. 7,1999, and U.S. Pat. No. 5,952,170 issued Jan. 17, 1995).

[0267] Additionally, one can examine the methylation status of a213P1F11 gene in a biological sample. Aberrant demethylation and/orhypermethylation of CpG islands in gene 5′ regulatory regions frequentlyoccurs in immortalized and transformed cells, and can result in alteredexpression of various genes. For example, promoter hypermethylation ofthe pi-class glutathione S-transferase (a protein expressed in normalprostate but not expressed in >90% of prostate carcinomas) appears topermanently silence transcription of this gene and is the mostfrequently detected genomic alteration in prostate carcinomas (De Marzoet al., Am. J. Pathol. 155(6): 1985-1992 (1999)). In addition, thisalteration is present in at least 70% of cases of high-grade prostaticintraepithelial neoplasia (PIN) (Brooks et al., Cancer Epidemiol.Biomarkers Prev., 1998, 7:531-536). In another example, expression ofthe LAGE-I tumor specific gene (which is not expressed in normalprostate but is expressed in 25-50% of prostate cancers) is induced bydeoxy-azacytidine in lymphoblastoid cells, suggesting that tumoralexpression is due to demethylation (Lethe et al., Int. J. Cancer 76(6):903-908 (1998)). A variety of assays for examining methylation status ofa gene are well known in the art. For example, one can utilize, inSouthern hybridization approaches, methylation-sensitive restrictionenzymes that cannot cleave sequences that contain methylated CpG sitesto assess the methylation status of CpG islands. In addition, MSP(methylation specific PCR) can rapidly profile the methylation status ofall the CpG sites present in a CpG island of a given gene. Thisprocedure involves initial modification of DNA by sodium bisulfite(which will convert all umethylated cytosines to uracil) followed byamplification using primers specific for methylated versus unmethylatedDNA. Protocols involving methylation interference can also be found forexample in Current Protocols In Molecular Biology, Unit 12, Frederick M.Ausubel et al. eds., 1995.

[0268] Gene amplification is an additional method for assessing thestatus of 213P1F11. Gene amplification is measured in a sample directly,for example, by conventional Southern blotting or Northern blotting toquantitate the transcription of mRNA (Thomas, 1980, Proc. Natl. Acad.Sci. USA, 77:5201-5205), dot blotting (DNA analysis), or in situhybridization, using an appropriately labeled probe, based on thesequences provided herein. Alternatively, antibodies are employed thatrecognize specific duplexes, including DNA duplexes, RNA duplexes, andDNA-RNA hybrid duplexes or DNA-protein duplexes. The antibodies in turnare labeled and the assay carried out where the duplex is bound to asurface, so that upon the formation of duplex on the surface, thepresence of antibody bound to the duplex can be detected.

[0269] Biopsied tissue or peripheral blood can be conveniently assayedfor the presence of cancer cells using for example, Northern, dot blotor RT-PCR analysis to detect 213P1F11 expression. The presence of RT-PCRamplifiable 213P1F11 mRNA provides an indication of the presence ofcancer. RT-PCR assays are well known in the art. RT-PCR detection assaysfor tumor cells in peripheral blood are currently being evaluated foruse in the diagnosis and management of a number of human solid tumors.In the prostate cancer field, these include RT-PCR assays for thedetection of cells expressing PSA and PSM (Verkaik et al., 1997, Urol.Res. 25:373-384; Ghossein et al, 1995, J. Clin. Oncol. 13:1195-2000;Heston et al., 1995, Clin. Chem. 41:1687-1688).

[0270] A further aspect of the invention is an assessment of thesusceptibility that an individual has for developing cancer. In oneembodiment, a method for predicting susceptibility to cancer comprisesdetecting 213P1F11 mRNA or 213P1F11 protein in a tissue sample, itspresence indicating susceptibility to cancer, wherein the degree of213P1F11 mRNA expression correlates to the degree of susceptibility. Ina specific embodiment, the presence of 213P1F11 in prostate or othertissue is examined, with the presence of 213P1F11 in the sampleproviding an indication of prostate cancer susceptibility (or theemergence or existence of a prostate tumor). Similarly, one can evaluatethe integrity 213P1F11 nucleotide and amino acid sequences in abiological sample, in order to identify perturbations in the structureof these molecules such as insertions, deletions, substitutions and thelike. The presence of one or more perturbations in 213P1F11 geneproducts in the sample is an indication of cancer susceptibility (or theemergence or existence of a tumor).

[0271] The invention also comprises methods for gauging tumoraggressiveness. In one embodiment, a method for gauging aggressivenessof a tumor comprises determining the level of 213P1F11 mRNA or 213P1F11protein expressed by tumor cells, comparing the level so determined tothe level of 213P1F11 mRNA or 213P1F11 protein expressed in acorresponding normal tissue taken from the same individual or a normaltissue reference sample, wherein the degree of 213P1F11 mRNA or 213P1F11protein expression in the tumor sample relative to the normal sampleindicates the degree of aggressiveness. In a specific embodiment,aggressiveness of a tumor is evaluated by determining the extent towhich 213P1F11 is expressed in the tumor cells, with higher expressionlevels indicating more aggressive tumors. Another embodiment is theevaluation of the integrity of 213P1F11 nucleotide and amino acidsequences in a biological sample, in order to identify perturbations inthe structure of these molecules such as insertions, deletions,substitutions and the like. The presence of one or more perturbationsindicates more aggressive tumors.

[0272] Another embodiment of the invention is directed to methods forobserving the progression of a malignancy in an individual over time. Inone embodiment, methods for observing the progression of a malignancy inan individual over time comprise determining the level of 213P1F11 mRNAor 213P1F11 protein expressed by cells in a sample of the tumor,comparing the level so determined to the level of 213P1F11 mRNA or213P1F11 protein expressed in an equivalent tissue sample taken from thesame individual at a different time, wherein the degree of 213P1F11 mRNAor 213P1F11 protein expression in the tumor sample over time providesinformation on the progression of the cancer. In a specific embodiment,the progression of a cancer is evaluated by determining 213P1F11expression in the tumor cells over time, where increased expression overtime indicates a progression of the cancer. Also, one can evaluate theintegrity 213P1F11 nucleotide and amino acid sequences in a biologicalsample in order to identify perturbations in the structure of thesemolecules such as insertions, deletions, substitutions and the like,where the presence of one or more perturbations indicates a progressionof the cancer.

[0273] The above diagnostic approaches can be combined with any one of awide variety of prognostic and diagnostic protocols known in the art.For example, another embodiment of the invention is directed to methodsfor observing a coincidence between the expression of 213P1F11 gene and213P1F11 gene products (or perturbations in 213P1F11 gene and 213P1F11gene products) and a factor that is associated with malignancy, as ameans for diagnosing and prognosticating the status of a tissue sample.A wide variety of factors associated with malignancy can be utilized,such as the expression of genes associated with malignancy (e.g. PSA,PSCA and PSM expression for prostate cancer etc.) as well as grosscytological observations (see, e.g., Bocking et al, 1984, Anal. Quant.Cytol. 6(2):74-88; Epstein, 1995, Hum. Pathol. 26(2):223-9; Thorson etal, 1998, Mod. Pathol. 11(6):543-51; Baisden et al, 1999, Am. J. Surg.Pathol. 23(8):918-24). Methods for observing a coincidence between theexpression of 213P1F11 gene and 213P1F11 gene products (or perturbationsin 213P1F11 gene and 213P1F11 gene products) and another factor that isassociated with malignancy are useful, for example, because the presenceof a set of specific factors that coincide with disease providesinformation crucial for diagnosing and prognosticating the status of atissue sample.

[0274] In one embodiment, methods for observing a coincidence betweenthe expression of 213P1F11 gene and 213P1F11 gene products (orperturbations in 213P1F11 gene and 213P1F11 gene products) and anotherfactor associated with malignancy entails detecting the overexpressionof 213P1F11 mRNA or protein in a tissue sample, detecting theoverexpression of PSA mRNA or protein in a tissue sample (or PSCA or PSMexpression), and observing a coincidence of 213P1F11 mRNA or protein andPSA mRNA or protein overexpression (or PSCA or PSM expression). In aspecific embodiment, the expression of 213P1F11 and PSA mRNA in prostatetissue is examined, where the coincidence of 213P1F11 and PSA mRNAoverexpression in the sample indicates the existence of prostate cancer,prostate cancer susceptibility or the emergence or status of a prostatetumor.

[0275] Methods for detecting and quantifying the expression of 213P1F11mRNA or protein are described herein, and standard nucleic acid andprotein detection and quantification technologies are well known in theart. Standard methods for the detection and quantification of 213P1F11mRNA include in situ hybridization using labeled 213P1F11 riboprobes,Northern blot and related techniques using 213P1F11 polynucleotideprobes, RT-PCR analysis using primers specific for 213P1F11, and otheramplification type detection methods, such as, for example, branchedDNA, SISBA, TMA and the like. In a specific embodiment,semi-quantitative RT-PCR is used to detect and quantify 213P1F11 mRNAexpression. Any number of primers capable of amplifying 213P1F11 can beused for this purpose, including but not limited to the various primersets specifically described herein. In a specific embodiment, polyclonalor monoclonal antibodies specifically reactive with the wild-type213P1F11 protein can be used in an immunohistochemical assay of biopsiedtissue.

[0276] IX.) Identification of Molecules That Interact With 213P1F11

[0277] The 213P1F11 protein and nucleic acid sequences disclosed hereinallow a skilled artisan to identify proteins, small molecules and otheragents that interact with 213P1F11, as well as pathways activated by213P1F11 via any one of a variety of art accepted protocols. Forexample, one can utilize one of the so-called interaction trap systems(also referred to as the “two-hybrid assay”). In such systems, moleculesinteract and reconstitute a transcription factor which directsexpression of a reporter gene, whereupon the expression of the reportergene is assayed. Other systems identify protein-protein interactions invivo through reconstitution of a eukaryotic transcriptional activator,see, e.g., U.S. Pat. No. 5,955,280 issued Sep. 21, 1999, U.S. Pat. No.5,925,523 issued Jul. 20, 1999, U.S. Pat. No. 5,846,722 issued Dec. 8,1998 and 6,004,746 issued Dec. 21, 1999. Algorithms are also availablein the art for genome-based predictions of protein function (see, e.g.,Marcotte, et al., Nature 402: Nov. 4, 1999, 83-86).

[0278] Alternatively one can screen peptide libraries to identifymolecules that interact with 213P1F11 protein sequences. In suchmethods, peptides that bind to 213P1F11 are identified by screeninglibraries that encode a random or controlled collection of amino acids.Peptides encoded by the libraries are expressed as fusion proteins ofbacteriophage coat proteins, the bacteriophage particles are thenscreened against the 213P1F11 protein(s).

[0279] Accordingly, peptides having a wide variety of uses, such astherapeutic, prognostic or diagnostic reagents, are thus identifiedwithout any prior information on the structure of the expected ligand orreceptor molecule. Typical peptide libraries and screening methods thatcan be used to identify molecules that interact with 213P1F11 proteinsequences are disclosed for example in U.S. Pat. No. 5,723,286 issuedMar. 3, 1998 and U.S. Pat. No. 5,733,731 issued Mar. 31, 1998.

[0280] Alternatively, cell lines that express 213P1F11 are used toidentify protein-protein interactions mediated by 213P1F11. Suchinteractions can be examined using immunoprecipitation techniques (see,e.g., Hamilton B. J., et al. Biochem. Biophys. Res. Commun. 1999,261:646-51). 213P1F11 protein can be immunoprecipitated from213P1F11-expressing cell lines using anti-213P1F11 antibodies.Alternatively, antibodies against His-tag can be used in a cell lineengineered to express fusions of 213P1F11 and a His-tag (vectorsmentioned above). The immunoprecipitated complex can be examined forprotein association by procedures such as Western blotting,³⁵S-methionine labeling of proteins, protein microsequencing, silverstaining and two-dimensional gel electrophoresis.

[0281] Small molecules and ligands that interact with 213P1F11 can beidentified through related embodiments of such screening assays. Forexample, small molecules can be identified that interfere with proteinfunction, including molecules that interfere with 213P1F11's ability tomediate phosphorylation and de-phosphorylation, interaction with DNA orRNA molecules as an indication of regulation of cell cycles, secondmessenger signaling or tumorigenesis. Similarly, small molecules thatmodulate 213P1F11-related ion channel, protein pump, or cellcommunication functions are identified and used to treat patients thathave a cancer that expresses 213P1F11 (see, e.g., Hille, B., IonicChannels of Excitable Membranes 2^(nd) Ed., Sinauer Assoc., Sunderland,Mass., 1992). Moreover, ligands that regulate 213P1F11 function can beidentified based on their ability to bind 213P1F11 and activate areporter construct. Typical methods are discussed for example in U.S.Pat. No. 5,928,868 issued Jul. 27, 1999, and include methods for forminghybrid ligands in which at least one ligand is a small molecule. In anillustrative embodiment, cells engineered to express a fusion protein of213P1F11 and a DNA-binding protein are used to co-express a fusionprotein of a hybrid ligand/small molecule and a cDNA librarytranscriptional activator protein. The cells further contain a reportergene, the expression of which is conditioned on the proximity of thefirst and second fusion proteins to each other, an event that occursonly if the hybrid ligand binds to target sites on both hybrid proteins.Those cells that express the reporter gene are selected and the unknownsmall molecule or the unknown ligand is identified. This method providesa means of identifying modulators which activate or inhibit 213P1F11.

[0282] An embodiment of this invention comprises a method of screeningfor a molecule that interacts with a 213P1F11 amino acid sequence shownin FIG. 2 or FIG. 3, comprising the steps of contacting a population ofmolecules with a 213P1F11 amino acid sequence, allowing the populationof molecules and the 213P1F11 amino acid sequence to interact underconditions that facilitate an interaction, determining the presence of amolecule that interacts with the 213P1F11 amino acid sequence, and thenseparating molecules that do not interact with the 213P1F11 amino acidsequence from molecules that do. In a specific embodiment, the methodfurther comprises purifying, characterizing and identifying a moleculethat interacts with the 213P1F11 amino acid sequence. The identifiedmolecule can be used to modulate a function performed by 213P1F11. In apreferred embodiment, the 213P1F11 amino acid sequence is contacted witha library of peptides.

[0283] X.) Therapeutic Methods and Compositions

[0284] The identification of 213P1F11 as a protein that is normallyexpressed in a restricted set of tissues, but which is also expressed inprostate and other cancers, opens a number of therapeutic approaches tothe treatment of such cancers. As contemplated herein, 213P1F11functions as a transcription factor involved in activatingtumor-promoting genes or repressing genes that block tumorigenesis.

[0285] Accordingly, therapeutic approaches that inhibit the activity ofa 213P1F11 protein are useful for patients suffering from a cancer thatexpresses 213P1F11. These therapeutic approaches generally fall into twoclasses. One class comprises various methods for inhibiting the bindingor association of a 213P1F11 protein with its binding partner or withother proteins. Another class comprises a variety of methods forinhibiting the transcription of a 213P1F11 gene or translation of213P1F11 mRNA.

[0286] X.A.) Anti-Cancer Vaccines

[0287] The invention provides cancer vaccines comprising a213P1F11-related protein or 213P1F11-related nucleic acid. In view ofthe expression of 213P1F11, cancer vaccines prevent and/or treat213P1F11-expressing cancers with minimal or no effects on non-targettissues. The use of a tumor antigen in a vaccine that generates humoraland/or cell-mediated immune responses as anti-cancer therapy is wellknown in the art and has been employed in prostate cancer using humanPSMA and rodent PAP immunogens (Hodge et al., 1995, Int. J. Cancer63:231-237; Fong et al, 1997, J. Immunol. 159:3113-3117).

[0288] Such methods can be readily practiced by employing a213P1F11-related protein, or a 213P1F11-encoding nucleic acid moleculeand recombinant vectors capable of expressing and presenting the213P1F11 immunogen (which typically comprises a number of antibody or Tcell epitopes). Skilled artisans understand that a wide variety ofvaccine systems for delivery of immunoreactive epitopes are known in theart (see, e.g., Heryln et al., Ann Med February 1999 31(1):66-78;Maruyama et al., Cancer Immunol Immunother June 2000 49(3):123-32)Briefly, such methods of generating an immune response (e.g. humoraland/or cell-mediated) in a mammal, comprise the steps of: exposing themammal's immune system to an immunoreactive epitope (e.g. an epitopepresent in a 213P1F11 protein shown in FIG. 3 or analog or homologthereof) so that the mammal generates an immune response that isspecific for that epitope (e.g. generates antibodies that specificallyrecognize that epitope). In a preferred method, a 213P1F11 immunogencontains a biological motif, see e.g., Tables V-XIX, or a peptide of asize range from 213P1F11 indicated in FIG. 5, FIG. 6, FIG. 7, FIG. 8,and FIG. 9.

[0289] The entire 213P1F11 protein, immunogenic regions or epitopesthereof can be combined and delivered by various means. Such vaccinecompositions can include, for example, lipopeptides (e.g., Vitiello, A.et al., J. Clin. Invest. 95:341, 1995), peptide compositionsencapsulated in poly(DL-lactide-co-glycolide) (“PLG”) microspheres (see,e.g., Eldridge, et al., Molec. Immunol. 28:287-294, 1991: Alonso et al.,Vaccine 12:299-306, 1994; Jones et al., Vaccine 13:675-681, 1995),peptide compositions contained in immune stimulating complexes (ISCOMS)(see, e.g., Takahashi et al., Nature 344:873-875, 1990; Hu et al., ClinExp Immunol. 113:235-243, 1998), multiple antigen peptide systems (MAPs)(see e.g., Tarn, J. P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413,1988; Tam, J. P., J. Immunol. Methods 196:17-32, 1996), peptidesformulated as multivalent peptides; peptides for use in ballisticdelivery systems, typically crystallized peptides, viral deliveryvectors (Perkus, M. E. et al., In: Concepts in vaccine development,Kauftnann, S. H. E., ed., p. 379, 1996; Chakrabarti, S. et al., Nature320:535, 1986; Hu, S. L. et al., Nature 320:537, 1986; Kieny, M.-P. etal., AIDS Bio/Technology 4:790, 1986; Top, F. H. et al., J. Infect. Dis.124:148, 1971; Chanda, P. K. et al., Virology 175:535, 1990), particlesof viral or synthetic origin (e.g., Kofler, N. et al., J. Immunol.Methods. 192:25, 1996; Eldridge, J. H. et al., Sem. Hematol. 30:16,1993; Falo, L. D., Jr. et al., Nature Med. 7:649, 1995), adjuvants(Warren, H. S., Vogel, F. R., and Chedid, L. A. Annu. Rev. Immunol.4:369, 1986; Gupta, R. K. et al., Vaccine 11:293, 1993), liposomes(Reddy, R. et al., J. Immunol. 148:1585, 1992; Rock, K. L., Immunol.Today 17:131, 1996), or, naked or particle absorbed cDNA (Ulmer, J. B.et al., Science 259:1745, 1993; Robinson, H. L., Hunt, L. A., andWebster, R. G., Vaccine 11:957, 1993; Shiver, J. W. et al., In: Conceptsin vaccine development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K.B., and Berzofsky, J. A., Annu. Rev. Immunol. 12:923, 1994 and Eldridge,J. H. et al., Sem. Hematol. 30:16, 1993). Toxin-targeted deliverytechnologies, also known as receptor mediated targeting, such as thoseof Avant Immunotherapeutics, Inc. (Needham, Mass.) may also be used.

[0290] In patients with 213P1F11-associated cancer, the vaccinecompositions of the invention can also be used in conjunction with othertreatments used for cancer, e.g., surgery, chemotherapy, drug therapies,radiation therapies, etc. including use in combination with immuneadjuvants such as IL-2, IL-12, GM-CSF, and the like.

[0291] Cellular Vaccines:

[0292] CTL epitopes can be determined using specific algorithms toidentify peptides within 213P1F11 protein that bind corresponding HLAalleles (see e.g., Table IV; Epimer™ and Epimatrix™, Brown University(URL www.brown.edu/Researcb/TB-HIV_Lab/epimatrix/epimatrix.html); and,BIMAS, (URL bimas.dcrt.nih.gov/; SYFPEITHI at URLsyfpeithi.bmi-heidelberg.com/). In a preferred embodiment, a 213P1F11immunogen contains one or more amino acid sequences identified usingtechniques well known in the art, such as the sequences shown in TablesV-XIX, or a peptide of 8, 9, 10 or 11 amino acids specified by an HLAClass I motif/supermotif (e.g., Table IV (A), Table IV (D), or Table IV(E)) and/or a peptide of at least 9 amino acids that comprises an HLAClass II motif/supermotif (e.g., Table IV (B) or Table IV (C)). As isappreciated in the art, the HLA Class I binding groove is essentiallyclosed ended so that peptides of only a particular size range can fitinto the groove and be bound, generally HLA Class I epitopes are 8, 9,10, or 11 amino acids long. In contrast, the HLA Class II binding grooveis essentially open ended; therefore a peptide of about 9 or more aminoacids can be bound by an HLA Class II molecule. Due to the bindinggroove differences between HLA Class I and II, HLA Class I motifs arelength specific, i.e., position two of a Class I motif is the secondamino acid in an amino to carboxyl direction of the peptide. The aminoacid positions in a Class II motif are relative only to each other, notthe overall peptide, i.e., additional amino acids can be attached to theamino and/or carboxyl termini of a motif-bearing sequence. HLA Class IIepitopes are often 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, or 25 amino acids long, or longer than 25 amino acids.

[0293] Antibody-Based Vaccines

[0294] A wide variety of methods for generating an immune response in amammal are known in the art (for example as the first step in thegeneration of hybridomas). Methods of generating an immune response in amammal comprise exposing the mammal's immune system to an immunogenicepitope on a protein (e.g. a 213P1F11 protein) so that an immuneresponse is generated. A typical embodiment consists of a method forgenerating an immune response to 213P1F11 in a host, by contacting thehost with a sufficient amount of at least one 213P1F11 B cell orcytotoxic T-cell epitope or analog thereof, and at least one periodicinterval thereafter re-contacting the host with the 213P1F11 B cell orcytotoxic T-cell epitope or analog thereof. A specific embodimentconsists of a method of generating an immune response against a213P1F11-related protein or a man-made multiepitopic peptide comprising:administering 213P1F11 immunogen (e.g. a 213P1F11 protein or a peptidefragment thereof, a 213P1F11 fusion protein or analog etc.) in a vaccinepreparation to a human or another mammal. Typically, such vaccinepreparations further contain a suitable adjuvant (see, e.g., U.S. Pat.No. 6,146,635) or a universal helper epitope such as a PADRE™ peptide(Epimmune Inc., San Diego, Calif.; see, e.g., Alexander et al., J.Immunol. 2000 164(3); 164(3): 1625-1633; Alexander et al., Immunity 19941(9): 751-761 and Alexander et al., Immunol. Res. 1998 18(2): 79-92). Analternative method comprises generating an immune response in anindividual against a 213P1F11 immunogen by: administering in vivo tomuscle or skin of the individual's body a DNA molecule that comprises aDNA sequence that encodes a 213P1F11 immunogen, the DNA sequenceoperatively linked to regulatory sequences which control the expressionof the DNA sequence; wherein the DNA molecule is taken up by cells, theDNA sequence is expressed in the cells and an immune response isgenerated against the immunogen (see, e.g., U.S. Pat. No. 5,962,428).Optionally a genetic vaccine facilitator such as anionic lipids;saponins; lectins; estrogenic compounds; hydroxylated lower alkyls;dimethyl sulfoxide; and urea is also administered. In addition, anantiidiotypic antibody can be administered that mimics 213P1F11, inorder to generate a response to the target antigen.

[0295] Nucleic Acid Vaccines:

[0296] Vaccine compositions of the invention include nucleicacid-mediated modalities. DNA or RNA that encode protein(s) of theinvention can be administered to a patient. Genetic immunization methodscan be employed to generate prophylactic or therapeutic humoral andcellular immune responses directed against cancer cells expressing213P1F11. Constructs comprising DNA encoding a 213P1F11-relatedprotein/immunogen and appropriate regulatory sequences can be injecteddirectly into muscle or skin of an individual, such that the cells ofthe muscle or skin take-up the construct and express the encoded213P1F11 protein/immunogen. Alternatively, a vaccine comprises a213P1F11-related protein. Expression of the 213P1F11-related proteinimmunogen results in the generation of prophylactic or therapeutichumoral and cellular immunity against cells that bear a 213P1F11protein. Various prophylactic and therapeutic genetic immunizationtechniques known in the art can be used (for review, see information andreferences published at Internet address www.genweb.com). Nucleicacid-based delivery is described, for instance, in Wolff et. al.,Science 247:1465 (1990) as well as U.S. Pat. Nos. 5,580,859; 5,589,466;5,804,566; 5,739,118; 5,736,524; 5,679,647; WO 98/04720. Examples ofDNA-based delivery technologies include “naked DNA”, facilitated(bupivicaine, polymers, peptide-mediated) delivery, cationic lipidcomplexes, and particle-mediated (“gene gun”) or pressure-mediateddelivery (see, e.g., U.S. Pat. No. 5,922,687).

[0297] For therapeutic or prophylactic immunization purposes, proteinsof the invention can be expressed via viral or bacterial vectors.Various viral gene delivery systems that can be used in the practice ofthe invention include, but are not limited to, vaccinia, fowlpox,canarypox, adenovirus, influenza, poliovirus, adeno-associated virus,lentivirus, and sindbis virus (see, e.g., Restifo, 1996, Curr. Opin.Immunol. 8:658-663; Tsang et al. J. Natl. Cancer Inst. 87:982-990(1995)). Non-viral delivery systems can also be employed by introducingnaked DNA encoding a 213P1F11-related protein into the patient (e.g.,intramuscularly or intradermally) to induce an anti-tumor response.

[0298] Vaccinia virus is used, for example, as a vector to expressnucleotide sequences that encode the peptides of the invention. Uponintroduction into a host, the recombinant vaccinia virus expresses theprotein immunogenic peptide, and thereby elicits a host immune response.Vaccinia vectors and methods useful in immunization protocols aredescribed in, e.g., U.S. Pat. No. 4,722,848. Another vector is BCG(Bacille Calmette Guerin). BCG vectors are described in Stover et al.,Nature 351:456-460 (1991). A wide variety of other vectors useful fortherapeutic administration or immunization of the peptides of theinvention, e.g. adeno and adeno-associated virus vectors, retroviralvectors, Salmonella typhi vectors, detoxified anthrax toxin vectors, andthe like, will be apparent to those skilled in the art from thedescription herein.

[0299] Thus, gene delivery systems are used to deliver a213P1F11-related nucleic acid molecule. In one embodiment, thefull-length human 213P1F11 cDNA is employed. In another embodiment,213P1F11 nucleic acid molecules encoding specific cytotoxic T lymphocyte(CTL) and/or antibody epitopes are employed.

[0300] Ex Vivo Vaccines

[0301] Various ex vivo strategies can also be employed to generate animmune response. One approach involves the use of antigen presentingcells (APCs) such as dendritic cells (DC) to present 213P1F11 antigen toa patient's immune system. Dendritic cells express MHC class I and IImolecules, B7 co-stimulator, and IL-12, and are thus highly specializedantigen presenting cells. In prostate cancer, autologous dendritic cellspulsed with peptides of the prostate-specific membrane antigen (PSMA)are being used in a Phase I clinical trial to stimulate prostate cancerpatients' immune systems (Tjoa et al., 1996, Prostate 28:65-69; Murphyet al., 1996, Prostate 29:371-380). Thus, dendritic cells can be used topresent 213P1F11 peptides to T cells in the context of MHC class I or IImolecules. In one embodiment, autologous dendritic cells are pulsed with213P1F11 peptides capable of binding to MHC class I and/or class IImolecules. In another embodiment, dendritic cells are pulsed with thecomplete 213P1F11 protein. Yet another embodiment involves engineeringthe overexpression of a 213P1F11 gene in dendritic cells using variousimplementing vectors known in the art, such as adenovirus (Arthur etal., 1997, Cancer Gene Ther. 4:17-25), retrovirus (Henderson et al.,1996, Cancer Res. 56:3763-3770), lentivirus, adeno-associated virus, DNAtransfection (Ribas et al., 1997, Cancer Res. 57:2865-2869), ortumor-derived RNA transfection (Ashley et al., 1997, J. Exp. Med.186:1177-1182). Cells that express 213P1F11 can also be engineered toexpress immune modulators, such as GM-CSF, and used as immunizingagents.

[0302] X.B.) 213P1F11 as a Target for Antibody-based Therapy

[0303] 213P1F11 is an attractive target for antibody-based therapeuticstrategies. A number of antibody strategies are known in the art fortargeting both extracellular and intracellular molecules (see, e.g.,complement and ADCC mediated killing as well as the use of intrabodies).Because 213P1F11 is expressed by cancer cells of various lineagesrelative to corresponding normal cells, systemic administration of213P1F11-immunoreactive compositions are prepared that exhibit excellentsensitivity without toxic, non-specific and/or non-target effects causedby binding of the immunoreactive composition to non-target organs andtissues. Antibodies specifically reactive with domains of 213P1F11 areuseful to treat 213P1F11-expressing cancers systemically, either asconjugates with a toxin or therapeutic agent, or as naked antibodiescapable of inhibiting cell proliferation or function.

[0304] 213P1F11 antibodies can be introduced into a patient such thatthe antibody binds to 213P1F11 and modulates a function, such as aninteraction with a binding partner, and consequently mediatesdestruction of the tumor cells and/or inhibits the growth of the tumorcells. Mechanisms by which such antibodies exert a therapeutic effectcan include complement-mediated cytolysis, antibody-dependent cellularcytotoxicity, modulation of the physiological function of 213P1F11,inhibition of ligand binding or signal transduction pathways, modulationof tumor cell differentiation, alteration of tumor angiogenesis factorprofiles, and/or apoptosis.

[0305] Those skilled in the art understand that antibodies can be usedto specifically target and bind immunogenic molecules such as animmunogenic region of a 213P1F11 sequence shown in FIG. 2 or FIG. 3. Inaddition, skilled artisans understand that it is routine to conjugateantibodies to cytotoxic agents (see, e.g., Slevers et al. Blood 93:113678-3684 (Jun. 1, 1999)). When cytotoxic and/or therapeutic agents aredelivered directly to cells, such as by conjugating them to antibodiesspecific for a molecule expressed by that cell (e.g. 213P1F11), thecytotoxic agent will exert its known biological effect (i.e.cytotoxicity) on those cells.

[0306] A wide variety of compositions and methods for usingantibody-cytotoxic agent conjugates to kill cells are known in the art.In the context of cancers, typical methods entail administering to ananimal having a tumor a biologically effective amount of a conjugatecomprising a selected cytotoxic and/or therapeutic agent linked to atargeting agent (e.g. an anti-213P1F11 antibody) that binds to a marker(e.g. 213P1F11) expressed, accessible to binding or localized on thecell surfaces. A typical embodiment is a method of delivering acytotoxic and/or therapeutic agent to a cell expressing 213P1F11,comprising conjugating the cytotoxic agent to an antibody thatimmunospecifically binds to a 213P1F11 epitope, and, exposing the cellto the antibody-agent conjugate. Another illustrative embodiment is amethod of treating an individual suspected of suffering frommetastasized cancer, comprising a step of administering parenterally tosaid individual a pharmaceutical composition comprising atherapeutically effective amount of an antibody conjugated to acytotoxic and/or therapeutic agent.

[0307] Cancer immunotherapy using anti-213P1F11 antibodies can be donein accordance with various approaches that have been successfullyemployed in the treatment of other types of cancer, including but notlimited to colon cancer (Arlen et al, 1998, Crit. Rev. Immunol.18:133-138), multiple myeloma (Ozaki et al., 1997, Blood 90:3179-3186,Tsunenari et al., 1997, Blood 90:2437-2444), gastric cancer (Kasprzyk etal, 1992, Cancer Res. 52:2771-2776), B-cell lymphoma (Funakoshi et al.,1996, J. Immunother. Emphasis Tumor Immunol. 19:93-101), leukemia (Zhonget al., 1996, Leuk. Res. 20:581-589), colorectal cancer (Moun et al,1994, Cancer Res. 54:6160-6166; Velders et al, 1995, Cancer Res.55:4398-4403), and breast cancer (Shepard et al., 1991, J. Clin.Immunol. 11:117-127). Some therapeutic approaches involve conjugation ofnaked antibody to a toxin or radioisotope, such as the conjugation ofY⁹¹ or I¹³¹ to anti-CD20 antibodies (e.g., Zevalin™, IDECPharmaceuticals Corp. or Bexxar™, Coulter Pharmaceuticals), while othersinvolve co-administration of antibodies and other therapeutic agents,such as Herceptin™ (trastuzumab) with paclitaxel (Genentech, Inc.). Theantibodies can be conjugated to a therapeutic agent. To treat prostatecancer, for example, 213P1F11 antibodies can be administered inconjunction with radiation, chemotherapy or hormone ablation. Also,antibodies can be conjugated to a toxin such as calicheamicin (e.g.,Mylotarg™, Wyeth-Ayerst, Madison, N.J., a recombinant humanized IgG₄kappa antibody conjugated to antitumor antibiotic calicheamicin) or amaytansinoid (e.g., taxane-based Tumor-Activated Prodrug, TAP, platform,ImmunoGen, Cambridge, Mass., also see e.g., U.S. Pat. No. 5,416,064).

[0308] Although 213P1F11 antibody therapy is useful for all stages ofcancer, antibody therapy can be particularly appropriate in advanced ormetastatic cancers. Treatment with the antibody therapy of the inventionis indicated for patients who have received one or more rounds ofchemotherapy. Alternatively, antibody therapy of the invention iscombined with a chemotherapeutic or radiation regimen for patients whohave not received chemotherapeutic treatment. Additionally, antibodytherapy can enable the use of reduced dosages of concomitantchemotherapy, particularly for patients who do not tolerate the toxicityof the chemotherapeutic agent very well. Fan et al. (Cancer Res.53:4637-4642, 1993), Prewett et al. (International J. of Onco.9:217-224, 1996), and Hancock et al. (Cancer Res. 51:4575-4580, 1991)describe the use of various antibodies together with chemotherapeuticagents.

[0309] Although 213P1F11 antibody therapy is useful for all stages ofcancer, antibody therapy can be particularly appropriate in advanced ormetastatic cancers. Treatment with the antibody therapy of the inventionis indicated for patients who have received one or more rounds ofchemotherapy. Alternatively, antibody therapy of the invention iscombined with a chemotherapeutic or radiation regimen for patients whohave not received chemotherapeutic treatment. Additionally, antibodytherapy can enable the use of reduced dosages of concomitantchemotherapy, particularly for patients who do not tolerate the toxicityof the chemotherapeutic agent very well.

[0310] Cancer patients can be evaluated for the presence and level of213P1F11 expression, preferably using immunohistochemical assessments oftumor tissue, quantitative 213P1F11 imaging, or other techniques thatreliably indicate the presence and degree of 213P1F11 expression.Immunohistochemical analysis of tumor biopsies or surgical specimens ispreferred for this purpose. Methods for immunohistochemical analysis oftumor tissues are well known in the art.

[0311] Anti-213P1F11 monoclonal antibodies that treat prostate and othercancers include those that initiate a potent immune response against thetumor or those that are directly cytotoxic. In this regard,anti-213P1F11 monoclonal antibodies (mAbs) can elicit tumor cell lysisby either complement-mediated or antibody-dependent cell cytotoxicity(ADCC) mechanisms, both of which require an intact Fc portion of theimmunoglobulin molecule for interaction with effector cell Fc receptorsites on complement proteins. In addition, anti-213P1F11 mAbs that exerta direct biological effect on tumor growth are useful to treat cancersthat express 213P1F11. Mechanisms by which directly cytotoxic mAbs actinclude: inhibition of cell growth, modulation of cellulardifferentiation, modulation of tumor angiogenesis factor profiles, andthe induction of apoptosis. The mechanism(s) by which a particularanti-213P1F11 mAb exerts an anti-tumor effect is evaluated using anynumber of in vitro assays that evaluate cell death such as ADCC, ADMMC,complement-mediated cell lysis, and so forth, as is generally known inthe art.

[0312] In some patients, the use of murine or other non-human monoclonalantibodies, or human/mouse chimeric mAbs can induce moderate to strongimmune responses against the non-human antibody. This can result inclearance of the antibody from circulation and reduced efficacy. In themost severe cases, such an immune response can lead to the extensiveformation of immune complexes which, potentially, can cause renalfailure. Accordingly, preferred monoclonal antibodies used in thetherapeutic methods of the invention are those that are either fullyhuman or humanized and that bind specifically to the target 213P1F11antigen with high affinity but exhibit low or no antigenicity in thepatient.

[0313] Therapeutic methods of the invention contemplate theadministration of single anti-213P1F11 mabs as well as combinations, orcocktails, of different mAbs. Such mAb cocktails can have certainadvantages inasmuch as they contain mAbs that target different epitopes,exploit different effector mechanisms or combine directly cytotoxic mAbswith mAbs that rely on immune effector functionality. Such mAbs incombination can exhibit synergistic therapeutic effects. In addition,anti-213P1F11 mAbs can be administered concomitantly with othertherapeutic modalities, including but not limited to variouschemotherapeutic agents, androgen-blockers, immune modulators (e.g.,IL-2, GM-CSF), surgery or radiation. The anti-213P1F11 mAbs areadministered in their “naked” or unconjugated form, or can have atherapeutic agent(s) conjugated to them.

[0314] Anti-213P1F11 antibody formulations are administered via anyroute capable of delivering the antibodies to a tumor cell. Routes ofadministration include, but are not limited to, intravenous,intraperitoneal, intramuscular, intratumor, intradermal, and the like.Treatment generally involves repeated administration of theanti-213P1F11 antibody preparation, via an acceptable route ofadministration such as intravenous injection (IV), typically at a dosein the range of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9., 1,2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 mg/kg body weight. In general,doses in the range of 10-1000 mg mAb per week are effective and welltolerated.

[0315] Based on clinical experience with the Herceptin™ mAb in thetreatment of metastatic breast cancer, an initial loading dose ofapproximately 4 mg/kg patient body weight IV, followed by weekly dosesof about 2 mg/kg IV of the anti-213P1F11 mAb preparation represents anacceptable dosing regimen. Preferably, the initial loading dose isadministered as a 90 minute or longer infusion. The periodic maintenancedose is administered as a 30 minute or longer infusion, provided theinitial dose was well tolerated. As appreciated by those of skill in theart, various factors can influence the ideal dose regimen in aparticular case. Such factors include, for example, the binding affinityand half life of the Ab or mAbs used, the degree of 213P1F11 expressionin the patient, the extent of circulating shed 213P1F11 antigen, thedesired steady-state antibody concentration level, frequency oftreatment, and the influence of chemotherapeutic or other agents used incombination with the treatment method of the invention, as well as thehealth status of a particular patient.

[0316] Optionally, patients should be evaluated for the levels of213P1F11 in a given sample (e.g. the levels of circulating 213P1F11antigen and/or 213P1F11 expressing cells) in order to assist in thedetermination of the most effective dosing regimen, etc. Suchevaluations are also used for monitoring purposes throughout therapy,and are useful to gauge therapeutic success in combination with theevaluation of other parameters (for example, urine cytology and/orImmunoCyt levels in bladder cancer therapy, or by analogy, serum PSAlevels in prostate cancer therapy).

[0317] Anti-idiotypic anti-213P1F11 antibodies can also be used inanti-cancer therapy as a vaccine for inducing an immune response tocells expressing a 213P1F11-related protein. In particular, thegeneration of anti-idiotypic antibodies is well known in the art; thismethodology can readily be adapted to generate anti-idiotypicanti-213P1F11 antibodies that mimic an epitope on a 213P1F11-relatedprotein (see, for example, Wagner et al, 1997, Hybridoma 16: 33-40; Foonet al, 1995, J. Clin. Invest. 96:334-342; Herlyn et al, 1996, CancerImmunol. Immunother. 43:65-76). Such an anti-idiotypic antibody can beused in cancer vaccine strategies.

[0318] X.C.) 213P1F11 as a Target for Cellular Immune Responses

[0319] Vaccines and methods of preparing vaccines that contain animmunogenically effective amount of one or more HLA-binding peptides asdescribed herein are further embodiments of the invention. Furthermore,vaccines in accordance with the invention encompass compositions of oneor more of the claimed peptides. A peptide can be present in a vaccineindividually. Alternatively, the peptide can exist as a homopolymercomprising multiple copies of the same peptide, or as a heteropolymer ofvarious peptides. Polymers have the advantage of increased immunologicalreaction and, where different peptide epitopes are used to make up thepolymer, the additional ability to induce antibodies and/or CTLs thatreact with different antigenic determinants of the pathogenic organismor tumor-related peptide targeted for an immune response. Thecomposition can be a naturally occurring region of an antigen or can beprepared, e.g., recombinantly or by chemical synthesis.

[0320] Carriers that can be used with vaccines of the invention are wellknown in the art, and include, e.g., thyroglobulin, albumins such ashuman serum albumin, tetanus toxoid, polyamino acids such as polyL-lysine, poly L-glutamic acid, influenza, hepatitis B virus coreprotein, and the like. The vaccines can contain a physiologicallytolerable (i.e., acceptable) diluent such as water, or saline,preferably phosphate buffered saline. The vaccines also typicallyinclude an adjuvant. Adjuvants such as incomplete Freund's adjuvant,aluminum phosphate, aluminum hydroxide, or alum are examples ofmaterials well known in the art. Additionally, as disclosed herein, CTLresponses can be primed by conjugating peptides of the invention tolipids, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine (P₃CSS).Moreover, an adjuvant such as a syntheticcytosine-phosphorothiolated-guanine-containing (CpG) oligonucleotideshas been found to increase CTL responses 10- to 100-fold. (see, e.g.Davila and Celis, J. Immunol. 165:539-547 (2000))

[0321] Upon immunization with a peptide composition in accordance withthe invention, via injection, aerosol, oral, transdermal, transmucosal,intrapleural, intrathecal, or other suitable routes, the immune systemof the host responds to the vaccine by producing large amounts of CTLsand/or HTLs specific for the desired antigen. Consequently, the hostbecomes at least partially immune to later development of cells thatexpress or overexpress 213P1F11 antigen, or derives at least sometherapeutic benefit when the antigen was tumor-associated.

[0322] In some embodiments, it may be desirable to combine the class Ipeptide components with components that induce or facilitateneutralizing antibody and or helper T cell responses directed to thetarget antigen. A preferred embodiment of such a composition comprisesclass I and class II epitopes in accordance with the invention. Analternative embodiment of such a composition comprises a class I and/orclass II epitope in accordance with the invention, along with a crossreactive HTL epitope such as PADRE™ (Epimmune, San Diego, Calif.)molecule (described e.g., in U.S. Pat. No. 5,736,142).

[0323] A vaccine of the invention can also include antigen-presentingcells (APC), such as dendritic cells (DC), as a vehicle to presentpeptides of the invention. Vaccine compositions can be created in vitro,following dendritic cell mobilization and harvesting, whereby loading ofdendritic cells occurs in vitro. For example, dendritic cells aretransfected, e.g., with a minigene in accordance with the invention, orare pulsed with peptides. The dendritic cell can then be administered toa patient to elicit immune responses in vivo. Vaccine compositions,either DNA- or peptide-based, can also be administered in vivo incombination with dendritic cell mobilization whereby loading ofdendritic cells occurs in vivo.

[0324] Preferably, the following principles are utilized when selectingan array of epitopes for inclusion in a polyepitopic composition for usein a vaccine, or for selecting discrete epitopes to be included in avaccine and/or to be encoded by nucleic acids such as a minigene. It ispreferred that each of the following principles be balanced in order tomake the selection. The multiple epitopes to be incorporated in a givenvaccine composition may be, but need not be, contiguous in sequence inthe native antigen from which the epitopes are derived.

[0325] 1.) Epitopes are selected which, upon administration, mimicimmune responses that have been observed to be correlated with tumorclearance. For HLA Class I this includes 3-4 epitopes that come from atleast one tumor associated antigen (TAA). For HLA Class II a similarrationale is employed; again 3-4 epitopes are selected from at least oneTAA (see, e.g., Rosenberg et al, Science 278:1447-1450). Epitopes fromone TAA may be used in combination with epitopes from one or moreadditional TAAs to produce a vaccine that targets tumors with varyingexpression patterns of frequently-expressed TAAs.

[0326] 2.) Epitopes are selected that have the requisite bindingaffinity established to be correlated with immunogenicity: for HLA ClassI an IC₅₀ of 500 nM or less, often 200 nM or less; and for Class II anIC₅₀ of 1000 nM or less.

[0327] 3.) Sufficient supermotif bearing-peptides, or a sufficient arrayof allele-specific motif-bearing peptides, are selected to give broadpopulation coverage. For example, it is preferable to have at least 80%population coverage. A Monte Carlo analysis, a statistical evaluationknown in the art, can be employed to assess the breadth, or redundancyof, population coverage.

[0328] 4.) When selecting epitopes from cancer-related antigens it isoften useful to select analogs because the patient may have developedtolerance to the native epitope.

[0329] 5.) Of particular relevance are epitopes referred to as “nestedepitopes.” Nested epitopes occur where at least two epitopes overlap ina given peptide sequence. A nested peptide sequence can comprise B cell,HLA class I and/or HLA class II epitopes. When providing nestedepitopes, a general objective is to provide the greatest number ofepitopes per sequence. Thus, an aspect is to avoid providing a peptidethat is any longer than the amino terminus of the amino terminal epitopeand the carboxyl terminus of the carboxyl terminal epitope in thepeptide. When providing a multi-epitopic sequence, such as a sequencecomprising nested epitopes, it is generally important to screen thesequence in order to insure that it does not have pathological or otherdeleterious biological properties.

[0330] 6.) If a polyepitopic protein is created, or when creating aminigene, an objective is to generate the smallest peptide thatencompasses the epitopes of interest. This principle is similar, if notthe same as that employed when selecting a peptide comprising nestedepitopes. However, with an artificial polyepitopic peptide, the sizeminimization objective is balanced against the need to integrate anyspacer sequences between epitopes in the polyepitopic protein. Spaceramino acid residues can, for example, be introduced to avoid junctionalepitopes (an epitope recognized by the immune system, not present in thetarget antigen, and only created by the man-made juxtaposition ofepitopes), or to facilitate cleavage between epitopes and therebyenhance epitope presentation. Junctional epitopes are generally to beavoided because the recipient may generate an immune response to thatnon-native epitope. Of particular concern is a junctional epitope thatis a “dominant epitope.” A dominant epitope may lead to such a zealousresponse that immune responses to other epitopes are diminished orsuppressed.

[0331] 7.) Where the sequences of multiple variants of the same targetprotein are present, potential peptide epitopes can also be selected onthe basis of their conservancy. For example, a criterion for conservancymay define that the entire sequence of an HLA class I binding peptide orthe entire 9-mer core of a class II binding peptide be conserved in adesignated percentage of the sequences evaluated for a specific proteinantigen.

[0332] X.C.1. Minigene Vaccines

[0333] A number of different approaches are available which allowsimultaneous delivery of multiple epitopes. Nucleic acids encoding thepeptides of the invention are a particularly useful embodiment of theinvention. Epitopes for inclusion in a minigene are preferably selectedaccording to the guidelines set forth in the previous section. Apreferred means of administering nucleic acids encoding the peptides ofthe invention uses minigene constructs encoding a peptide comprising oneor multiple epitopes of the invention.

[0334] The use of multi-epitope minigenes is described below and in,Ishioka et al., J. Immunol 162:3915-3925, 1999; An, L. and Whitton, J.L., J. Virol. 71:2292, 1997; Thomson, S. A. et al., J. Immunol 157:822,1996; Whitton, J. L. et al., J. Virol. 67:348, 1993; Hanke, R. et al.,Vaccine 16:426, 1998. For example, a multi-epitope DNA plasmid encodingsupermotif- and/or motif-bearing epitopes derived 213P1F11, the PADRE®universal helper T cell epitope or multiple HTL epitopes from 213P1F11(see e.g., Tables V-XIX), and an endoplasmic reticulum-translocatingsignal sequence can be engineered. A vaccine may also comprise epitopesthat are derived from other TAAs.

[0335] The immunogenicity of a multi-epitopic minigene can be confirmedin transgenic mice to evaluate the magnitude of CTL induction responsesagainst the epitopes tested. Further, the immunogenicity of DNA-encodedepitopes in vivo can be correlated with the in vitro responses ofspecific CTL lines against target cells transfected with the DNAplasmid. Thus, these experiments can show that the minigene serves toboth: 1.) generate a CTL response and 2.) that the induced CTLsrecognized cells expressing the encoded epitopes.

[0336] For example, to create a DNA sequence encoding the selectedepitopes (minigene) for expression in human cells, the amino acidsequences of the epitopes may be reverse translated. A human codon usagetable can be used to guide the codon choice for each amino acid. Theseepitope-encoding DNA sequences may be directly adjoined, so that whentranslated, a continuous polypeptide sequence is created. To optimizeexpression and/or immunogenicity, additional elements can beincorporated into the minigene design. Examples of amino acid sequencesthat can be reverse translated and included in the minigene sequenceinclude: HLA class I epitopes, HLA class II epitopes, antibody epitopes,a ubiquitination signal sequence, and/or an endoplasmic reticulumtargeting signal. In addition, HLA presentation of CTL and HTL epitopesmay be improved by including synthetic (e.g. poly-alanine) ornaturally-occurring flanking sequences adjacent to the CTL or HTLepitopes; these larger peptides comprising the epitope(s) are within thescope of the invention.

[0337] The minigene sequence may be converted to DNA by assemblingoligonucleotides that encode the plus and minus strands of the minigene.Overlapping oligonucleotides (30-100 bases long) may be synthesized,phosphorylated, purified and annealed under appropriate conditions usingwell known techniques. The ends of the oligonucleotides can be joined,for example, using T4 DNA ligase. This synthetic minigene, encoding theepitope polypeptide, can then be cloned into a desired expressionvector.

[0338] Standard regulatory sequences well known to those of skill in theart are preferably included in the vector to ensure expression in thetarget cells. Several vector elements are desirable: a promoter with adown-stream cloning site for minigene insertion; a polyadenylationsignal for efficient transcription termination; an E. coli origin ofreplication; and an E. coli selectable marker (e.g. ampicillin orkanamycin resistance). Numerous promoters can be used for this purpose,e.g., the human cytomegalovirus (hCMV) promoter. See, e.g., U.S. Pat.Nos. 5,580,859 and 5,589,466 for other suitable promoter sequences.

[0339] Additional vector modifications may be desired to optimizeminigene expression and immunogenicity. In some cases, introns arerequired for efficient gene expression, and one or more synthetic ornaturally-occurring introns could be incorporated into the transcribedregion of the minigene. The inclusion of mRNA stabilization sequencesand sequences for replication in mammalian cells may also be consideredfor increasing minigene expression.

[0340] Once an expression vector is selected, the minigene is clonedinto the polylinker region downstream of the promoter. This plasmid istransformed into an appropriate E. coli strain, and DNA is preparedusing standard techniques. The orientation and DNA sequence of theminigene, as well as all other elements included in the vector, areconfirmed using restriction mapping and DNA sequence analysis. Bacterialcells harboring the correct plasmid can be stored as a master cell bankand a working cell bank.

[0341] In addition, immunostimulatory sequences (ISSs or CpGs) appear toplay a role in the immunogenicity of DNA vaccines. These sequences maybe included in the vector, outside the minigene coding sequence, ifdesired to enhance immunogenicity.

[0342] In some embodiments, a bi-cistronic expression vector whichallows production of both the minigene-encoded epitopes and a secondprotein (included to enhance or decrease immunogenicity) can be used.Examples of proteins or polypeptides that could beneficially enhance theimmune response if co-expressed include cytokines (e.g., IL-2, IL-12,GM-CSF), cytokine-inducing molecules (e.g., LeIF), costimulatorymolecules, or for HTL responses, pan-DR binding proteins (PADRE™,Epimmune, San Diego, Calif.). Helper (HTL) epitopes can be joined tointracellular targeting signals and expressed separately from expressedCTL epitopes; this allows direction of the HTL epitopes to a cellcompartment different than that of the CTL epitopes. If required, thiscould facilitate more efficient entry of HTL epitopes into the HLA classII pathway, thereby improving HTL induction. In contrast to HTL or CTLinduction, specifically decreasing the immune response by co-expressionof immunosuppressive molecules (e.g. TGF-β) may be beneficial in certaindiseases.

[0343] Therapeutic quantities of plasmid DNA can be produced forexample, by fermentation in E. coli, followed by purification. Aliquotsfrom the working cell bank are used to inoculate growth medium, andgrown to saturation in shaker flasks or a bioreactor according towell-known techniques. Plasmid DNA can be purified using standardbioseparation technologies such as solid phase anion-exchange resinssupplied by QIAGEN, Inc. (Valencia, Calif.). If required, supercoiledDNA can be isolated from the open circular and linear forms using gelelectrophoresis or other methods.

[0344] Purified plasmid DNA can be prepared for injection using avariety of formulations. The simplest of these is reconstitution oflyophilized DNA in sterile phosphate-buffer saline (PBS). This approach,known as “naked DNA,” is currently being used for intramuscular (IM)administration in clinical trials. To maximize the immunotherapeuticeffects of minigene DNA vaccines, an alternative method for formulatingpurified plasmid DNA may be desirable. A variety of methods have beendescribed, and new techniques may become available. Cationic lipids,glycolipids, and fusogenic liposomes can also be used in the formulation(see, e.g., as described by WO 93/24640; Mannino & Gould-Fogerite,BioTechniques 6(7): 682 (1988); U.S. Pat. No. 5,279,833; WO 91/06309;and Felgner, et al., Proc. Nat'l Acad. Sci. USA 84:7413 (1987). Inaddition, peptides and compounds referred to collectively as protective,interactive, non-condensing compounds (PINC) could also be complexed topurified plasmid DNA to influence variables such as stability,intramuscular dispersion, or trafficking to specific organs or celltypes.

[0345] Target cell sensitization can be used as a functional assay forexpression and HLA class I presentation of minigene-encoded CTLepitopes. For example, the plasmid DNA is introduced into a mammaliancell line that is suitable as a target for standard CTL chromium releaseassays. The transfection method used will be dependent on the finalformulation. Electroporation can be used for “naked” DNA, whereascationic lipids allow direct in vitro transfection. A plasmid expressinggreen fluorescent protein (GFP) can be co-transfected to allowenrichment of transfected cells using fluorescence activated cellsorting (FACS). These cells are then chromium-51 (⁵¹Cr) labeled and usedas target cells for epitope-specific CTL lines; cytolysis, detected by⁵¹Cr release, indicates both production of, and HLA presentation of,minigene-encoded CTL epitopes. Expression of HTL epitopes may beevaluated in an analogous manner using assays to assess HTL activity.

[0346] In vivo immunogenicity is a second approach for functionaltesting of minigene DNA formulations. Transgenic mice expressingappropriate human HLA proteins are immunized with the DNA product. Thedose and route of administration are formulation dependent (e.g., IM forDNA in PBS, intraperitoneal (i.p.) for lipid-complexed DNA). Twenty-onedays after immunization, splenocytes are harvested and restimulated forone week in the presence of peptides encoding each epitope being tested.Thereafter, for CTL effector cells, assays are conducted for cytolysisof peptide-loaded, ⁵¹Cr-labeled target cells using standard techniques.Lysis of target cells that were sensitized by HLA loaded with peptideepitopes, corresponding to minigene-encoded epitopes, demonstrates DNAvaccine function for in vivo induction of CTLs. Immunogenicity of HTLepitopes is confirmed in transgenic mice in an analogous manner.

[0347] Alternatively, the nucleic acids can be administered usingballistic delivery as described, for instance, in U.S. Pat. No.5,204,253. Using this technique, particles comprised solely of DNA areadministered. In a further alternative embodiment, DNA can be adhered toparticles, such as gold particles.

[0348] Minigenes can also be delivered using other bacterial or viraldelivery systems well known in the art, e.g., an expression constructencoding epitopes of the invention can be incorporated into a viralvector such as vaccinia.

[0349] X.C.2. Combinations of CTL Peptides with Helper Peptides

[0350] Vaccine compositions comprising CTL peptides of the invention canbe modified, e.g., analoged, to provide desired attributes, such asimproved serum half life, broadened population coverage or enhancedimmunogenicity.

[0351] For instance, the ability of a peptide to induce CTL activity canbe enhanced by linking the peptide to a sequence which contains at leastone epitope that is capable of inducing a T helper cell response.Although a CTL peptide can be directly linked to a T helper peptide,often CTL epitope/HTL epitope conjugates are linked by a spacermolecule. The spacer is typically comprised of relatively small, neutralmolecules, such as amino acids or amino acid mimetics, which aresubstantially uncharged under physiological conditions. The spacers aretypically selected from, e.g., Ala, Gly, or other neutral spacers ofnonpolar amino acids or neutral polar amino acids. It will be understoodthat the optionally present spacer need not be comprised of the sameresidues and thus may be a hetero- or homo-oligomer. When present, thespacer will usually be at least one or two residues, more usually threeto six residues and sometimes 10 or more residues. The CTL peptideepitope can be linked to the T helper peptide epitope either directly orvia a spacer either at the amino or carboxy terminus of the CTL peptide.The amino terminus of either the immunogenic peptide or the T helperpeptide may be acylated.

[0352] In certain embodiments, the T helper peptide is one that isrecognized by T helper cells present in a majority of a geneticallydiverse population. This can be accomplished by selecting peptides thatbind to many, most, or all of the HLA class II molecules. Examples ofsuch amino acid bind many HLA Class II molecules include sequences fromantigens such as tetanus toxoid at positions 830-843 (QYIKANSKFIGITE;SEQ ID NO:______), Plasmodium falciparum circumsporozoite (CS) proteinat positions 378-398 (DIEKKIAKMEKASSVFNVVNS; SEQ ID NO:______), andStreptococcus 18 kD protein at positions 116-131 (GAVDSILGGVATYGAA; SEQID NO:______). Other examples include peptides bearing a DR 1-4-7supermotif, or either of the DR3 motifs.

[0353] Alternatively, it is possible to prepare synthetic peptidescapable of stimulating T helper lymphocytes, in a loosely HLA-restrictedfashion, using amino acid sequences not found in nature (see, e.g., PCTpublication WO 95/07707). These synthetic compounds calledPan-DR-binding epitopes (e.g., PADRE™, Epimmune, Inc., San Diego,Calif.) are designed to most preferably bind most HLA-DR (human HLAclass II) molecules. For instance, a pan-DR-binding epitope peptidehaving the formula: aKXVAAWTLKAAa (SEQ ID NO:______), where “X” iseither cyclohexylalanine, phenylalanine, or tyrosine, and a is eitherD-alanine or L-alanine, has been found to bind to most HLA-DR alleles,and to stimulate the response of T helper lymphocytes from mostindividuals, regardless of their HLA type. An alternative of a pan-DRbinding epitope comprises all “L” natural amino acids and can beprovided in the form of nucleic acids that encode the epitope.

[0354] HTL peptide epitopes can also be modified to alter theirbiological properties. For example, they can be modified to includeD-amino acids to increase their resistance to proteases and thus extendtheir serum half life, or they can be conjugated to other molecules suchas lipids, proteins, carbohydrates, and the like to increase theirbiological activity. For example, a T helper peptide can be conjugatedto one or more palmitic acid chains at either the amino or carboxyltermini.

[0355] X.C.3. Combinations of CTL Peptides with T Cell Priming Agents

[0356] In some embodiments it may be desirable to include in thepharmaceutical compositions of the invention at least one componentwhich primes B lymphocytes or T lymphocytes. Lipids have been identifiedas agents capable of priming CTL in vivo. For example, palmitic acidresidues can be attached to the ε-and α-amino groups of a lysine residueand then linked, e.g., via one or more linking residues such as Gly,Gly-Gly-, Ser, Ser-Ser, or the like, to an immunogenic peptide. Thelipidated peptide can then be administered either directly in a micelleor particle, incorporated into a liposome, or emulsified in an adjuvant,e.g., incomplete Freund's adjuvant. In a preferred embodiment, aparticularly effective immunogenic composition comprises palmitic acidattached to ε- and α-amino groups of Lys, which is attached via linkage,e.g., Ser-Ser, to the amino terminus of the immunogenic peptide.

[0357] As another example of lipid priming of CTL responses, E. colilipoproteins, such as tripalmitoyl-S-glycerylcysteinlyseryl-serine(P₃CSS) can be used to prime virus specific CTL when covalently attachedto an appropriate peptide (see, e.g., Deres, et al., Nature 342:561,1989). Peptides of the invention can be coupled to P₃CSS, for example,and the lipopeptide administered to an individual to specifically primean immune response to the target antigen. Moreover, because theinduction of neutralizing antibodies can also be primed withP₃CSS-conjugated epitopes, two such compositions can be combined to moreeffectively elicit both humoral and cell-mediated responses.

[0358] X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL and/orHTL Peptides

[0359] An embodiment of a vaccine composition in accordance with theinvention comprises ex vivo administration of a cocktail ofepitope-bearing peptides to PBMC, or isolated DC therefrom, from thepatient's blood. A pharmaceutical to facilitate harvesting of DC can beused, such as Progenipoietin™ (Pharmacia-Monsanto, St. Louis, Mo.) orGM-CSF/IL-4. After pulsing the DC with peptides and prior to reinfusioninto patients, the DC are washed to remove unbound peptides. In thisembodiment, a vaccine comprises peptide-pulsed DCs which present thepulsed peptide epitopes complexed with HLA molecules on their surfaces.

[0360] The DC can be pulsed ex vivo with a cocktail of peptides, some ofwhich stimulate CTL responses to 213P1F11. Optionally, a helper T cell(HTL) peptide, such as a natural or artificial loosely restricted HLAClass II peptide, can be included to facilitate the CTL response. Thus,a vaccine in accordance with the invention is used to treat a cancerwhich expresses or overexpresses 213P1F11.

[0361] X.D. Adoptive Immunotherapy

[0362] Antigenic 213P1F11-related peptides are used to elicit a CTLand/or HTL response ex vivo, as well. The resulting CTL or HTL cells,can be used to treat tumors in patients that do not respond to otherconventional forms of therapy, or will not respond to a therapeuticvaccine peptide or nucleic acid in accordance with the invention. Exvivo CTL or HTL responses to a particular antigen are induced byincubating in tissue culture the patient's, or genetically compatible,CTL or HTL precursor cells together with a source of antigen-presentingcells (APC), such as dendritic cells, and the appropriate immunogenicpeptide. After an appropriate incubation time (typically about 7-28days), in which the precursor cells are activated and expanded intoeffector cells, the cells are infused back into the patient, where theywill destroy (CTL) or facilitate destruction (HTL) of their specifictarget cell (e.g., a tumor cell). Transfected dendritic cells may alsobe used as antigen presenting cells.

[0363] X.E. Administration of Vaccines for Therapeutic or ProphylacticPurposes

[0364] Pharmaceutical and vaccine compositions of the invention aretypically used to treat and/or prevent a cancer that expresses oroverexpresses 213P1F11. In therapeutic applications, peptide and/ornucleic acid compositions are administered to a patient m an amountsufficient to elicit an effective B cell, CTL and/or HTL response to theantigen and to cure or at least partially arrest or slow symptoms and/orcomplications. An amount adequate to accomplish this is defined as“therapeutically effective dose.” Amounts effective for this use willdepend on, e.g., the particular composition administered, the manner ofadministration, the stage and severity of the disease being treated, theweight and general state of health of the patient, and the judgment ofthe prescribing physician.

[0365] For pharmaceutical compositions, the immunogenic peptides of theinvention, or DNA encoding them, are generally administered to anindividual already bearing a tumor that expresses 213P1F 11. Thepeptides or DNA encoding them can be administered individually or asfusions of one or more peptide sequences. Patients can be treated withthe immunogenic peptides separately or in conjunction with othertreatments, such as surgery, as appropriate.

[0366] For therapeutic use, administration should generally begin at thefirst diagnosis of 213P1F11-associated cancer. This is followed byboosting doses until at least symptoms are substantially abated and fora period thereafter. The embodiment of the vaccine composition (i.e.,including, but not limited to embodiments such as peptide cocktails,polyepitopic polypeptides, minigenes, or TAA-specific CTLs or pulseddendritic cells) delivered to the patient may vary according to thestage of the disease or the patient's health status. For example, in apatient with a tumor that expresses 213P1F11, a vaccine comprising213P1F11-specific CTL may be more efficacious in killing tumor cells inpatient with advanced disease than alternative embodiments.

[0367] It is generally important to provide an amount of the peptideepitope delivered by a mode of administration sufficient to effectivelystimulate a cytotoxic T cell response; compositions which stimulatehelper T cell responses can also be given in accordance with thisembodiment of the invention.

[0368] The dosage for an initial therapeutic immunization generallyoccurs in a unit dosage range where the lower value is about 1, 5, 50,500, or 1,000 μg and the higher value is about 10,000; 20,000; 30,000;or 50,000 μg. Dosage values for a human typically range from about 500μg to about 50,000 μg per 70 kilogram patient. Boosting dosages ofbetween about 1.0 μg to about 50,000 μg of peptide pursuant to aboosting regimen over weeks to months may be administered depending uponthe patient's response and condition as determined by measuring thespecific activity of CTL and HTL obtained from the patient's blood.Administration should continue until at least clinical symptoms orlaboratory tests indicate that the neoplasia, has been eliminated orreduced and for a period thereafter. The dosages, routes ofadministration, and dose schedules are adjusted in accordance withmethodologies known in the art.

[0369] In certain embodiments, the peptides and compositions of thepresent invention are employed in serious disease states, that is,life-threatening or potentially life threatening situations. In suchcases, as a result of the minimal amounts of extraneous substances andthe relative nontoxic nature of the peptides in preferred compositionsof the invention, it is possible and may be felt desirable by thetreating physician to administer substantial excesses of these peptidecompositions relative to these stated dosage amounts.

[0370] The vaccine compositions of the invention can also be used purelyas prophylactic agents. Generally the dosage for an initial prophylacticimmunization generally occurs in a unit dosage range where the lowervalue is about 1, 5, 50, 500, or 1000 μg and the higher value is about10,000; 20,000; 30,000; or 50,000 μg. Dosage values for a humantypically range from about 500 μg to about 50,000 μg per 70 kilogrampatient. This is followed by boosting dosages of between about 1.0 μg toabout 50,000 fig of peptide administered at defined intervals from aboutfour weeks to six months after the initial administration of vaccine.The immunogenicity of the vaccine can be assessed by measuring thespecific activity of CTL and HTL obtained from a sample of the patient'sblood.

[0371] The pharmaceutical compositions for therapeutic treatment areintended for parenteral, topical, oral, nasal, intrathecal, or local(e.g. as a cream or topical ointment) administration. Preferably, thepharmaceutical compositions are administered parentally, e.g.,intravenously, subcutaneously, intradermally, or intramuscularly. Thus,the invention provides compositions for parenteral administration whichcomprise a solution of the immunogenic peptides dissolved or suspendedin an acceptable carrier, preferably an aqueous carrier.

[0372] A variety of aqueous carriers may be used, e.g., water, bufferedwater, 0.8% saline, 0.3% glycine, hyaluronic acid and the like. Thesecompositions may be sterilized by conventional, well-known sterilizationtechniques, or may be sterile filtered. The resulting aqueous solutionsmay be packaged for use as is, or lyophilized, the lyophilizedpreparation being combined with a sterile solution prior toadministration.

[0373] The compositions may contain pharmaceutically acceptableauxiliary substances as required to approximate physiologicalconditions, such as pH-adjusting and buffering agents, tonicityadjusting agents, wetting agents, preservatives, and the like, forexample, sodium acetate, sodium lactate, sodium chloride, potassiumchloride, calcium chloride, sorbitan monolaurate, triethanolamineoleate, etc.

[0374] The concentration of peptides of the invention in thepharmaceutical formulations can vary widely, i.e., from less than about0.1%, usually at or at least about 2% to as much as 20% to 50% or moreby weight, and will be selected primarily by fluid volumes, viscosities,etc., in accordance with the particular mode of administration selected.

[0375] A human unit dose form of a composition is typically included ina pharmaceutical composition that comprises a human unit dose of anacceptable carrier, in one embodiment an aqueous carrier, and isadministered in a volume/quantity that is known by those of skill in theart to be used for administration of such compositions to humans (see,e.g., Remington's Pharmaceutical Sciences, 17^(th) Edition, A. Gennaro,Editor, Mack Publishing Co., Easton, Pa., 1985). For example a peptidedose for initial immunization can be from about 1 to about 50,000 μg,generally 100-5,000 μg, for a 70 kg patient. For example, for nucleicacids an initial immunization may be performed using an expressionvector in the form of naked nucleic acid administered IM (or SC or ID)in the amounts of 0.5-5 mg at multiple sites. The nucleic acid (0.1 to1000 μg) can also be administered using a gene gun. Following anincubation period of 3-4 weeks, a booster dose is then administered. Thebooster can be recombinant fowlpox virus administered at a dose of 5-10⁷to 5×10⁹ pfu.

[0376] For antibodies, a treatment generally involves repeatedadministration of the anti-213P1F11 antibody preparation, via anacceptable route of administration such as intravenous injection (IV),typically at a dose in the range of about 0.1 to about 10 mg/kg bodyweight. In general, doses in the range of 10-500 mg mAb per week areeffective and well tolerated. Moreover, an initial loading dose ofapproximately 4 mg/kg patient body weight IV, followed by weekly dosesof about 2 mg/kg IV of the anti-213P1F11 mAb preparation represents anacceptable dosing regimen. As appreciated by those of skill in the art,various factors can influence the ideal dose in a particular case. Suchfactors include, for example, half life of a composition, the bindingaffinity of an Ab, the immunogenicity of a substance, the degree of213P1F11 expression in the patient, the extent of circulating shed213P1F11 antigen, the desired steady-state concentration level,frequency of treatment, and the influence of chemotherapeutic or otheragents used in combination with the treatment method of the invention,as well as the health status of a particular patient. Non-limitingpreferred human unit doses are, for example, 500 μg-1 mg, 1 mg-50 mg, 50mg-100 mg, 100 mg-200 mg, 200 mg-300 mg, 400 mg-500 mg, 500 mg-600 mg,600 mg-700 mg, 700 mg-800 mg, 800 mg-900 mg, 900 mg-1 g, or 1 mg-700 mg.In certain embodiments, the dose is in a range of 2-5 mg/kg body weight,e.g., with follow on weekly doses of 1-3 mg/kg; 0.5 mg, 1, 2, 3, 4, 5,6, 7, 8, 9, 10 mg/kg body weight followed, e.g., in two, three or fourweeks by weekly doses; 0.5-10 mg/kg body weight, e.g., followed in two,three or four weeks by weekly doses; 225, 250, 275, 300, 325, 350, 375,400 mg m² of body area weekly; 1-600 mg m² of body area weekly; 225-400mg m² of body area weekly; these does can be followed by weekly dosesfor 2, 3, 4, 5, 6, 7, 8, 9, 19, 11, 12 or more weeks.

[0377] In one embodiment, human unit dose forms of polynucleotidescomprise a suitable dosage range or effective amount that provides anytherapeutic effect. As appreciated by one of ordinary skill in the art atherapeutic effect depends on a number of factors, including thesequence of the polynucleotide, molecular weight of the polynucleotideand route of administration. Dosages are generally selected by thephysician or other health care professional in accordance with a varietyof parameters known in the art, such as severity of symptoms, history ofthe patient and the like. Generally, for a polynucleotide of about 20bases, a dosage range may be selected from, for example, anindependently selected lower limit such as about 0.1, 0.25, 0.5, 1, 2,5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400 or 500 mg/kgup to an independently selected upper limit, greater than the lowerlimit, of about 60, 80, 100, 200, 300, 400, 500, 750, 1000, 1500, 2000,3000, 4000, 5000, 6000, 7000, 8000, 9000 or 10,000 mg/kg. For example, adose may be about any of the following: 0.1 to 100 mg/kg, 0.1 to 50mg/kg, 0.1 to 25 mg/kg, 0.1 to 10 mg/kg, 1 to 500 mg/kg, 100 to 400mg/kg, 200 to 300 mg/kg, 1 to 100 mg/kg, 100 to 200 mg/kg, 300 to 400mg/kg, 400 to 500 mg/kg, 500 to 1000 mg/kg, 500 to 5000 mg/kg, or 500 to10,000 mg/kg. Generally, parenteral routes of administration may requirehigher doses of polynucleotide compared to more direct application tothe nucleotide to diseased tissue, as do polynucleotides of increasinglength.

[0378] In one embodiment, human unit dose forms of T-cells comprise asuitable dosage range or effective amount that provides any therapeuticeffect. As appreciated by one of ordinary skill in the art, atherapeutic effect depends on a number of factors. Dosages are generallyselected by the physician or other health care professional inaccordance with a variety of parameters known in the art, such asseverity of symptoms, history of the patient and the like. A dose may beabout 10⁴ cells to about 10⁶ cells, about 10⁶ cells to about 10⁸ cells,about 10⁸ to about 10¹¹ cells, or about 10⁸ to about 5×10¹⁰ cells. Adose may also about 10⁶ cells/m² to about 10¹⁰ cells/m², or about 10⁶cells/m² to about 108 cells/m².

[0379] Proteins(s) of the invention, and/or nucleic acids encoding theprotein(s), can also be administered via liposomes, which may also serveto: 1) target the proteins(s) to a particular tissue, such as lymphoidtissue; 2) to target selectively to diseases cells; or, 3) to increasethe half-life of the peptide composition. Liposomes include emulsions,foams, micelles, insoluble monolayers, liquid crystals, phospholipiddispersions, lamellar layers and the like. In these preparations, thepeptide to be delivered is incorporated as part of a liposome, alone orin conjunction with a molecule which binds to a receptor prevalent amonglymphoid cells, such as monoclonal antibodies which bind to the CD45antigen, or with other therapeutic or immunogenic compositions. Thus,liposomes either filled or decorated with a desired peptide of theinvention can be directed to the site of lymphoid cells, where theliposomes then deliver the peptide compositions. Liposomes for use inaccordance with the invention are formed from standard vesicle-forminglipids, which generally include neutral and negatively chargedphospholipids and a sterol, such as cholesterol. The selection of lipidsis generally guided by consideration of, e.g., liposome size, acidlability and stability of the liposomes in the blood stream. A varietyof methods are available for preparing liposomes, as described in, e.g.,Szoka, et al, Ann. Rev. Biophys. Bioeng. 9:467 (1980), and U.S. Pat.Nos. 4,235,871, 4,501,728, 4,837,028, and 5,019,369.

[0380] For targeting cells of the immune system, a ligand to beincorporated into the liposome can include, e.g., antibodies orfragments thereof specific for cell surface determinants of the desiredimmune system cells. A liposome suspension containing a peptide may beadministered intravenously, locally, topically, etc. in a dose whichvaries according to, inter alia, the manner of administration, thepeptide being delivered, and the stage of the disease being treated.

[0381] For solid compositions, conventional nontoxic solid carriers maybe used which include, for example, pharmaceutical grades of mannitol,lactose, starch, magnesium stearate, sodium saccharin, talcum,cellulose, glucose, sucrose, magnesium carbonate, and the like. For oraladministration, a pharmaceutically acceptable nontoxic composition isformed by incorporating any of the normally employed excipients, such asthose carriers previously listed, and generally 10-95% of activeingredient, that is, one or more peptides of the invention, and morepreferably at a concentration of 25%-75%.

[0382] For aerosol administration, immunogenic peptides are preferablysupplied in finely divided form along with a surfactant and propellant.Typical percentages of peptides are about 0.01%-20% by weight,preferably about 1%-10%. The surfactant must, of course, be nontoxic,and preferably soluble in the propellant. Representative of such agentsare the esters or partial esters of fatty acids containing from about 6to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic,stearic, linoleic, linolenic, olesteric and oleic acids with analiphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, suchas mixed or natural glycerides may be employed. The surfactant mayconstitute about 0.1%-20% by weight of the composition, preferably about0.25-5%. The balance of the composition is ordinarily propellant. Acarrier can also be included, as desired, as with, e.g., lecithin forintranasal delivery.

[0383] XI.) Diagnostic and Prognostic Embodiments of 213P1F11.

[0384] As disclosed herein, 213P1F11 polynucleotides, polypeptides,reactive cytotoxic T cells (CTL), reactive helper T cells (HTL) andanti-polypeptide antibodies are used in well known diagnostic,prognostic and therapeutic assays that examine conditions associatedwith dysregulated cell growth such as cancer, in particular the cancerslisted in Table I (see, e.g., both its specific pattern of tissueexpression as well as its overexpression in certain cancers as describedfor example in the Example entitled “Expression Analysis of 213P1F11 inNormal Tissues and patient Specimens”).

[0385] 213P1F11 can be analogized to a prostate associated antigen PSA,the archetypal marker that has been used by medical practitioners foryears to identify and monitor the presence of prostate cancer (see,e.g., Merrill et al., J. Urol. 163(2): 503-5120 (2000); Polascik et al.,J. Urol. August; 162(2):293-306 (1999) and Fortier et al., J. Nat.Cancer Inst. 91(19): 1635-1640(1999)). A variety of other diagnosticmarkers are also used in similar contexts including p53 and K-ras (see,e.g., Tulchinsky et al., Int J Mol Med July 1999 4(1):99-102 andMinimoto et al., Cancer Detect Prev 2000;24(1):1-12). Therefore, thisdisclosure of 213P1F11 polynucleotides and polypeptides (as well as213P1F11 polynucleotide probes and anti-213P1F11 antibodies used toidentify the presence of these molecules) and their properties allowsskilled artisans to utilize these molecules in methods that areanalogous to those used, for example, in a variety of diagnostic assaysdirected to examining conditions associated with cancer.

[0386] Typical embodiments of diagnostic methods which utilize the213P1F11 polynucleotides, polypeptides, reactive T cells and antibodiesare analogous to those methods from well-established diagnostic assayswhich employ, e.g., PSA polynucleotides, polypeptides, reactive T cellsand antibodies. For example, just as PSA polynucleotides are used asprobes (for example in Northern analysis, see, e.g., Sharief et al.,Biochem. Mol. Biol. Int. 33(3):567-74(1994)) and primers (for example inPCR analysis, see, e.g., Okegawa et al., J. Urol. 163(4): 1189-1190(2000)) to observe the presence and/or the level of PSA mRNAs in methodsof monitoring PSA overexpression or the metastasis of prostate cancers,the 213P1F11 polynucleotides described herein can be utilized in thesame way to detect 213P1F11 overexpression or the metastasis of prostateand other cancers expressing this gene. Alternatively, just as PSApolypeptides are used to generate antibodies specific for PSA which canthen be used to observe the presence and/or the level of PSA proteins inmethods to monitor PSA protein overexpression (see, e.g., Stephan etal., Urology 55(4):560-3 (2000)) or the metastasis of prostate cells(see, e.g., Alanen et al., Pathol. Res. Pract. 192(3):233-7 (1996)), the213P1F11 polypeptides described herein can be utilized to generateantibodies for use in detecting 213P1F11 overexpression or themetastasis of prostate cells and cells of other cancers expressing thisgene.

[0387] Specifically, because metastases involves the movement of cancercells from an organ of origin (such as the lung or prostate gland etc.)to a different area of the body (such as a lymph node), assays whichexamine a biological sample for the presence of cells expressing213P1F11 polynucleotides and/or polypeptides can be used to provideevidence of metastasis. For example, when a biological sample fromtissue that does not normally contain 213P1F11-expressing cells (lymphnode) is found to contain 213P1F11-expressing cells such as the 213P1F11expression seen in LAPC4 and LAPC9, xenografts isolated from lymph nodeand bone metastasis, respectively, this finding is indicative ofmetastasis.

[0388] Alternatively 213P1F11 polynucleotides and/or polypeptides can beused to provide evidence of cancer, for example, when cells in abiological sample that do not normally express 213P1F11 or express213P1F11 at a different level are found to express 213P1F11 or have anincreased expression of 213P1F11 (see, e.g., the 213P1F11 expression inthe cancers listed in Table I and in patient samples etc. shown in theaccompanying Figures). In such assays, artisans may further wish togenerate supplementary evidence of metastasis by testing the biologicalsample for the presence of a second tissue restricted marker (inaddition to 213P1F11) such as PSA, PSCA etc. (see, e.g., Alanen et al,Pathol. Res. Pract. 192(3): 233-237 (1996)).

[0389] Just as PSA polynucleotide fragments and polynucleotide variantsare employed by skilled artisans for use in methods of monitoring PSA,213P1F11 polynucleotide fragments and polynucleotide variants are usedin an analogous manner. In particular, typical PSA polynucleotides usedin methods of monitoring PSA are probes or primers which consist offragments of the PSA cDNA sequence. Illustrating this, primers used toPCR amplify a PSA polynucleotide must include less than the whole PSAsequence to function in the polymerase chain reaction. In the context ofsuch PCR reactions, skilled artisans generally create a variety ofdifferent polynucleotide fragments that can be used as primers in orderto amplify different portions of a polynucleotide of interest or tooptimize amplification reactions (see, e.g., Caetano-Anolles, G.Biotechniques 25(3): 472-476, 478-480 (1998); Robertson et al, MethodsMol. Biol. 98:121-154 (1998)). An additional illustration of the use ofsuch fragments is provided in the Example entitled “Expression Analysisof 213P1F11 in Normal Tissues and Patient Specimens,” where a 213P1F11polynucleotide fragment is used as a probe to show the expression of213P1F11 RNAs in cancer cells. In addition, variant polynucleotidesequences are typically used as primers and probes for the correspondingmRNAs in PCR and Northern analyses (see, e.g., Sawai et al., FetalDiagn. Ther. 1996 Nov-Dec 11(6):407-13 and Current Protocols InMolecular Biology, Volume 2, Unit 2, Frederick M. Ausubel et al eds.,1995)). Polynucleotide fragments and variants are useful in this contextwhere they are capable of binding to a target polynucleotide sequence(e.g., a 213P1F11 polynucleotide shown in FIG. 2 or variant thereof)under conditions of high stringency.

[0390] Furthermore, PSA polypeptides which contain an epitope that canbe recognized by an antibody or T cell that specifically binds to thatepitope are used in methods of monitoring PSA. 213P1F11 polypeptidefragments and polypeptide analogs or variants can also be used in ananalogous manner. This practice of using polypeptide fragments orpolypeptide variants to generate antibodies (such as anti-PSA antibodiesor T cells) is typical in the art with a wide variety of systems such asfusion proteins being used by practitioners (see, e.g., CurrentProtocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubelet al. eds., 1995). In this context, each epitope(s) functions toprovide the architecture with which an antibody or T cell is reactive.Typically, skilled artisans create a variety of different polypeptidefragments that can be used in order to generate immune responsesspecific for different portions of a polypeptide of interest (see, e.g.,U.S. Pat. No. 5,840,501 and U.S. Pat. No. 5,939,533). For example it maybe preferable to utilize a polypeptide comprising one of the 213P1F11biological motifs discussed herein or a motif-bearing subsequence whichis readily identified by one of skill in the art based on motifsavailable in the art. Polypeptide fragments, variants or analogs aretypically useful in this context as long as they comprise an epitopecapable of generating an antibody or T cell specific for a targetpolypeptide sequence (e.g. a 213P1F11 polypeptide shown in FIG. 3).

[0391] As shown herein, the 213P1F11 polynucleotides and polypeptides(as well as the 213P1F11 polynucleotide probes and anti-213P1F11antibodies or T cells used to identify the presence of these molecules)exhibit specific properties that make them useful in diagnosing cancerssuch as those listed in Table I. Diagnostic assays that measure thepresence of 213P1F11 gene products, in order to evaluate the presence oronset of a disease condition described herein, such as prostate cancer,are used to identify patients for preventive measures or furthermonitoring, as has been done so successfully with PSA. Moreover, thesematerials satisfy a need in the art for molecules having similar orcomplementary characteristics to PSA in situations where, for example, adefinite diagnosis of metastasis of prostatic origin cannot be made onthe basis of a test for PSA alone (see, e.g., Alanen et al, Pathol. Res.Pract. 192(3): 233-237 (1996)), and consequently, materials such as213P1F11 polynucleotides and polypeptides (as well as the 213P1F11polynucleotide probes and anti-213P1F11 antibodies used to identify thepresence of these molecules) need to be employed to confirm a metastasesof prostatic origin.

[0392] Finally, in addition to their use in diagnostic assays, the213P1F11 polynucleotides disclosed herein have a number of otherutilities such as their use in the identification of oncogeneticassociated chromosomal abnormalities in the chromosomal region to whichthe 213P1F11 gene maps (see the Example entitled “Chromosomal Mapping of213P1F11” below). Moreover, in addition to their use in diagnosticassays, the 213P1F11-related proteins and polynucleotides disclosedherein have other utilities such as their use in the forensic analysisof tissues of unknown origin (see, e.g., Takahama K Forensic Sci IntJun. 28, 1996;80(1-2): 63-9).

[0393] Additionally, 213P1F11-related proteins or polynucleotides of theinvention can be used to treat a pathologic condition characterized bythe over-expression of 213P1F11. For example, the amino acid or nucleicacid sequence of FIG. 2 or FIG. 3, or fragments of either, can be usedto generate an immune response to a 213P1F11 antigen. Antibodies orother molecules that react with 213P1F11 can be used to modulate thefunction of this molecule, and thereby provide a therapeutic benefit.

[0394] XII.) Inhibition of 213P1F11 Protein Function

[0395] The invention includes various methods and compositions forinhibiting the binding of 213P1F11 to its binding partner or itsassociation with other protein(s) as well as methods for inhibiting213P1F11 function.

[0396] XII.A.) Inhibition of 213P1F11 With Intracellular Antibodies

[0397] In one approach, a recombinant vector that encodes single chainantibodies that specifically bind to 213P1F11 are introduced into213P1F11 expressing cells via gene transfer technologies. Accordingly,the encoded single chain anti-213P1F11 antibody is expressedintracellularly, binds to 213P1F11 protein, and thereby inhibits itsfunction. Methods for engineering such intracellular single chainantibodies are well known. Such intracellular antibodies, also known as“intrabodies”, are specifically targeted to a particular compartmentwithin the cell, providing control over where the inhibitory activity ofthe treatment is focused. This technology has been successfully appliedin the art (for review, see Richardson and Marasco, 1995, TIBTECH vol.13). Intrabodies have been shown to virtually eliminate the expressionof otherwise abundant cell surface receptors (see, e.g., Richardson etal., 1995, Proc. Natl. Acad. Sci. USA 92: 3137-3141; Beerli et al, 1994,J. Biol. Chem. 289: 23931-23936; Deshane et al, 1994, Gene Ther. 1:332-337).

[0398] Single chain antibodies comprise the variable domains of theheavy and light chain joined by a flexible linker polypeptide, and areexpressed as a single polypeptide. Optionally, single chain antibodiesare expressed as a single chain variable region fragment joined to thelight chain constant region. Well-known intracellular traffickingsignals are engineered into recombinant polynucleotide vectors encodingsuch single chain antibodies in order to precisely target the intrabodyto the desired intracellular compartment. For example, intrabodiestargeted to the endoplasmic reticulum (ER) are engineered to incorporatea leader peptide and, optionally, a C-terminal ER retention signal, suchas the KDEL amino acid motif. Intrabodies intended to exert activity inthe nucleus are engineered to include a nuclear localization signal.Lipid moieties are joined to intrabodies in order to tether theintrabody to the cytosolic side of the plasma membrane. Intrabodies canalso be targeted to exert function in the cytosol. For example,cytosolic intrabodies are used to sequester factors within the cytosol,thereby preventing them from being transported to their natural cellulardestination.

[0399] In one embodiment, intrabodies are used to capture 213P1F11 inthe nucleus, thereby preventing its activity within the nucleus. Nucleartargeting signals are engineered into such 213P1F11 intrabodies in orderto achieve the desired targeting. Such 213P1F11 intrabodies are designedto bind specifically to a particular 213P1F11 domain. In anotherembodiment, cytosolic intrabodies that specifically bind to a 213P1F11protein are used to prevent 213P1F P11 from gaining access to thenucleus, thereby preventing it from exerting any biological activitywithin the nucleus (e.g., preventing 213P1F11 from forming transcriptioncomplexes with other factors).

[0400] In order to specifically direct the expression of suchintrabodies to particular cells, the transcription of the intrabody isplaced under the regulatory control of an appropriate tumor-specificpromoter and/or enhancer. In order to target intrabody expressionspecifically to prostate, for example, the PSA promoter and/orpromoter/enhancer can be utilized (See, for example, U.S. Pat. No.5,919,652 issued Jul. 6, 1999).

[0401] XII.B.) Inhibition of 213P1F11 with Recombinant Proteins

[0402] In another approach, recombinant molecules bind to 213P1F11 andthereby inhibit 213P1F11 function. For example, these recombinantmolecules prevent or inhibit 213P1F11 from accessing/binding to itsbinding partner(s) or associating with other protein(s). Suchrecombinant molecules can, for example, contain the reactive part(s) ofa 213P1F11 specific antibody molecule. In a particular embodiment, the213P1F11 binding domain of a 213P1F11 binding partner is engineered intoa dimeric fusion protein, whereby the fusion protein comprises two213P1F11 ligand binding domains linked to the Fc portion of a human IgG,such as human IgG1. Such IgG portion can contain, for example, theC_(H)2 and C_(H)3 domains and the hinge region, but not the C_(H)1domain. Such dimeric fusion proteins are administered in soluble form topatients suffering from a cancer associated with the expression of213P1F11, whereby the dimeric fusion protein specifically binds to213P1F11 and blocks 213P1F11 interaction with a binding partner. Suchdimeric fusion proteins are further combined into multimeric proteinsusing known antibody linking technologies.

[0403] XII.C.) Inhibition of 213P1F11 Transcription or Translation

[0404] The present invention also comprises various methods andcompositions for inhibiting the transcription of the 213P1F11 gene.Similarly, the invention also provides methods and compositions forinhibiting the translation of 213P1F11 mRNA into protein.

[0405] In one approach, a method of inhibiting the transcription of the213P1F11 gene comprises contacting the 213P1F11 gene with a 213P1F11antisense polynucleotide. In another approach, a method of inhibiting213P1F11 mRNA translation comprises contacting a 213P1F11 mRNA with anantisense polynucleotide. In another approach, a 213P1F11 specificribozyme is used to cleave a 213P1F11 message, thereby inhibitingtranslation. Such antisense and ribozyme based methods can also bedirected to the regulatory regions of the 213P1F11 gene, such as213P1F11 promoter and/or enhancer elements. Similarly, proteins capableof inhibiting a 213P1F11 gene transcription factor are used to inhibit213P1F11F11 mRNA transcription. The various polynucleotides andcompositions useful in the aforementioned methods have been describedabove. The use of antisense and ribozyme molecules to inhibittranscription and translation is well known in the art.

[0406] Other factors that inhibit the transcription of 213P1F11 byinterfering with 213P1F11 transcriptional activation are also useful totreat cancers expressing 213P1F11. Similarly, factors that interferewith 213P1F11 processing are useful to treat cancers that express213P1F11. Cancer treatment methods utilizing such factors are alsowithin the scope of the invention.

[0407] XII.D.) General Considerations for Therapeutic Strategies

[0408] Gene transfer and gene therapy technologies can be used todeliver therapeutic polynucleotide molecules to tumor cells synthesizing213P1F11 (i.e., antisense, ribozyme, polynucleotides encodingintrabodies and other 213P1F11 inhibitory molecules). A number of genetherapy approaches are known in the art. Recombinant vectors encoding213P1F11 antisense polynucleotides, ribozymes, factors capable ofinterfering with 213P1F11 transcription, and so forth, can be deliveredto target tumor cells using such gene therapy approaches.

[0409] The above therapeutic approaches can be combined with any one ofa wide variety of surgical, chemotherapy or radiation therapy regimens.The therapeutic approaches of the invention can enable the use ofreduced dosages of chemotherapy (or other therapies) and/or lessfrequent administration, an advantage for all patients and particularlyfor those that do not tolerate the toxicity of the chemotherapeuticagent well.

[0410] The anti-tumor activity of a particular composition (e.g.,antisense, ribozyme, intrabody), or a combination of such compositions,can be evaluated using various in vitro and in vivo assay systems. Invitro assays that evaluate therapeutic activity include cell growthassays, soft agar assays and other assays indicative of tumor promotingactivity, binding assays capable of determining the extent to which atherapeutic composition will inhibit the binding of 213P1F11 to abinding partner, etc.

[0411] In vivo, the effect of a 213P1F11 therapeutic composition can beevaluated in a suitable animal model. For example, xenogenic prostatecancer models can be used, wherein human prostate cancer explants orpassaged xenograft tissues are introduced into immune compromisedanimals, such as nude or SCID mice (Klein et al., 1997, Nature Medicine3: 402-408). For example, PCT Patent Application WO98/16628 and U.S.Pat. No. 6,107,540 describe various xenograft models of human prostatecancer capable of recapitulating the development of primary tumors,micrometastasis, and the formation of osteoblastic metastasescharacteristic of late stage disease. Efficacy can be predicted usingassays that measure inhibition of tumor formation, tumor regression ormetastasis, and the like.

[0412] In vivo assays that evaluate the promotion of apoptosis areuseful in evaluating therapeutic compositions. In one embodiment,xenografts from tumor bearing mice treated with the therapeuticcomposition can be examined for the presence of apoptotic foci andcompared to untreated control xenograft-bearing mice. The extent towhich apoptotic foci are found in the tumors of the treated miceprovides an indication of the therapeutic efficacy of the composition.

[0413] The therapeutic compositions used in the practice of theforegoing methods can be formulated into pharmaceutical compositionscomprising a carrier suitable for the desired delivery method. Suitablecarriers include any material that when combined with the therapeuticcomposition retains the anti-tumor function of the therapeuticcomposition and is generally non-reactive with the patient's immunesystem. Examples include, but are not limited to, any of a number ofstandard pharmaceutical carriers such as sterile phosphate bufferedsaline solutions, bacteriostatic water, and the like (see, generally,Remington's Pharmaceutical Sciences 16^(th) Edition, A. Osal., Ed.,1980).

[0414] Therapeutic formulations can be solubilized and administered viaany route capable of delivering the therapeutic composition to the tumorsite. Potentially effective routes of administration include, but arenot limited to, intravenous, parenteral, intraperitoneal, intramuscular,intratumor, intradermal, intraorgan, orthotopic, and the like. Apreferred formulation for intravenous injection comprises thetherapeutic composition in a solution of preserved bacteriostatic water,sterile unpreserved water, and/or diluted in polyvinylchloride orpolyethylene bags containing 0.9% sterile Sodium Chloride for Injection,USP. Therapeutic protein preparations can be lyophilized and stored assterile powders, preferably under vacuum, and then reconstituted inbacteriostatic water (containing for example, benzyl alcoholpreservative) or in sterile water prior to injection.

[0415] Dosages and administration protocols for the treatment of cancersusing the foregoing methods will vary with the method and the targetcancer, and will generally depend on a number of other factorsappreciated in the art.

[0416] XIII.) Kits

[0417] For use in the diagnostic and therapeutic applications describedherein, kits are also within the scope of the invention. Such kits cancomprise a carrier, package or container that is compartmentalized toreceive one or more containers such as vials, tubes, and the like, eachof the container(s) comprising one of the separate elements to be usedin the method. For example, the container(s) can comprise a probe thatis or can be detectably labeled. Such probe can be an antibody orpolynucleotide specific for a 213P1F11-related protein or a 213P1F11gene or message, respectively. Where the method utilizes nucleic acidhybridization to detect the target nucleic acid, the kit can also havecontainers containing nucleotide(s) for amplification of the targetnucleic acid sequence and/or a container comprising a reporter-means,such as a biotin-binding protein, such as avidin or streptavidin, boundto a reporter molecule, such as an enzymatic, florescent, orradioisotope label. The kit can include all or part of the amino acidsequence of FIG. 2 or FIG. 3 or analogs thereof, or a nucleic acidmolecules that encodes such amino acid sequences.

[0418] The kit of the invention will typically comprise the containerdescribed above and one or more other containers comprising materialsdesirable from a commercial and user standpoint, including buffers,diluents, filters, needles, syringes, and package inserts withinstructions for use.

[0419] A label can be present on the container to indicate that thecomposition is used for a specific therapy or non-therapeuticapplication, and can also indicate directions for either in vivo or invitro use, such as those described above. Directions and or otherinformation can also be included on an insert which is included with thekit.

EXAMPLES

[0420] Various aspects of the invention are further described andillustrated by way of the several examples that follow, none of whichare intended to limit the scope of the invention.

Example 1 SSH-Generated Isolation of a cDNA Fragment of the 213P1F11Gene

[0421] To isolate genes that are over-expressed in bladder cancer,Suppression Subtractive Hybridization (SSH) procedure using cDNA derivedfrom bladder cancer tissues was performed, including invasivetransitional cell carcinoma. The 213P1F11 SSH cDNA sequence was derivedfrom a bladder cancer pool minus cDNAs derived from 9 normal tissues.The 213P1F11 cDNA was identified as highly expressed in the bladdercancer tissue pool, with no expression detected in normal tissues.

[0422] The SSH DNA sequence of 166 bp (FIG. 1) did not show homology toany known gene. 213P1F11v.1 of 3336 bp was identified and the openreading frame cloned from bladder cancer cDNA, revealing an ORF of 242amino acids (FIG. 2 and FIG. 3). Other variants of 213P1F11, were alsoidentified and these are listed in FIGS. 2 and 3. 213P1F11 v.1 reveals100% identity to caspase-14 precursor apoptosis-related cysteineprotease protein (FIG. 4).

[0423] Materials and Methods

[0424] Human Tissues:

[0425] The patient cancer and normal tissues were purchased fromdifferent sources such as the NDRI (Philadelphia, Pa.). mRNA forsome-normal tissues were purchased from Clontech, Palo Alto, Calif.

[0426] RNA Isolation:

[0427] Tissues were homogenized in Trizol reagent (Life Technologies,Gibco BRL) using 10 ml/g tissue isolate total RNA. Poly A RNA waspurified from total RNA using Qiagen's Oligotex mRNA Mini and Midi kits.Total and mRNA were quantified by spectrophotometric analysis (O.D.260/280 nm) and analyzed by gel electrophoresis.

[0428] Oligonucleotides:

[0429] The following HPLC purified oligonucleotides were used. DPNCDN(cDNA synthesis primer): (SEQ ID NO: 707) 5′TTTTGATCAAGCTT₃₀3′ Adaptor1: (SEQ ID NO: 708) 5′CTAATACGACTCACTATAGGGCTCGAGCGGCCGCCCGGGCAG3′ (SEQID NO: 708) 3′GGCCCGTCCTAG5′ Adaptor 2: (SEQ ID NO: 709)5′GTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAG3′ (SEQ ID NO: 710)3′CGGCTCCTAG5′ PCR primer 1: (SEQ ID NO: 711) 5′CTAATACGACTCACTATAGGGC3′Nested primer (NP)1: (SEQ ID NO: 712) 5′TCGAGCGGCCGCCCGGGCAGGA3′ Nestedprimer (NP)2: (SEQ ID NO: 713) 5′AGCGTGGTCGCGGCCGAGGA3′

[0430] Suppression Subtractive Hybridization:

[0431] Suppression Subtractive Hybridization (SSH) was used to identifycDNAs corresponding to genes that may be differentially expressed inbladder cancer. The SSH reaction utilized cDNA from bladder cancer andnormal tissues.

[0432] The gene 213P1F11 sequence was derived from a bladder cancer poolminus normal tissue cDNA subtraction. The SSH DNA sequence (FIG. 1) wasidentified.

[0433] The cDNA derived from of pool of normal tissues was used as thesource of the “driver” cDNA, while the cDNA from a pool of bladdercancer tissues was used as the source of the “tester” cDNA. Doublestranded cDNAs corresponding to tester and driver cDNAs were synthesizedfrom 2 μg of poly(A)⁺ RNA isolated from the relevant xenograft tissue,as described above, using CLONTECH's PCR-Select cDNA Subtraction Kit and1 ng of oligonucleotide DPNCDN as primer. First- and second-strandsynthesis were carried out as described in the Kit's user manualprotocol (CLONTECH Protocol No. PT1117-1, Catalog No. K1804-1). Theresulting cDNA was digested with Dpn II for 3 hrs at 37° C. DigestedcDNA was extracted with phenol/chloroform (1:1) and ethanolprecipitated.

[0434] Driver cDNA was generated by combining in a 1:1 ratio Dpn IIdigested cDNA from the relevant tissue source (see above) with a mix ofdigested cDNAs derived from the nine normal tissues: stomach, skeletalmuscle, lung, brain, liver, kidney, pancreas, small intestine, andheart.

[0435] Tester cDNA was generated by diluting 1 μl of Dpn II digestedcDNA from the relevant tissue source (see above) (400 ng) in 5 it ofwater. The diluted cDNA (2 μl, 160 ng) was then ligated to 2 μl ofAdaptor I and Adaptor 2 (10 μM), in separate ligation reactions, in atotal volume of 10 μl at 16° C. overnight, using 400 u of T4 DNA ligase(CLONTECH). Ligation was terminated with 1 μl of 0.2 M EDTA and heatingat 72° C. for 5 min.

[0436] The first hybridization was performed by adding 1.5 μl (600 ng)of driver cDNA to each of two tubes containing 1.5 μl (20 ng) Adaptor 1-and Adaptor 2-ligated tester cDNA. In a final volume of 4 μl, thesamples were overlaid with mineral oil, denatured in an MJ Researchthermal cycler at 98° C. for 1.5 minutes, and then were allowed tohybridize for 8 hrs at 68° C. The two hybridizations were then mixedtogether with an additional 1 μl of fresh denatured driver cDNA and wereallowed to hybridize overnight at 68° C. The second hybridization wasthen diluted in 200 μl of 20 mM Hepes, pH 8.3, 50 mM NaCl, 0.2 mM EDTA,heated at 70° C. for 7 min. and stored at −20° C.

[0437] PCR Amplification. Cloning and Sequencing of Gene FragmentsGenerated from SSH:

[0438] To amplify gene fragments resulting from SSH reactions, two PCRamplifications were performed. In the primary PCR reaction 1 μl of thediluted final hybridization mix was added to 1 μl of PCR primer 1 (10μM), 0.5 μl dNTP mix (10 μM), 2.5 μl 10× reaction buffer (CLONTECH) and0.5 μl 50× Advantage cDNA polymerase Mix (CLONTECH) in a final volume of25 μl. PCR 1 was conducted using the following conditions: 75° C. for 5min., 94° C. for 25 sec., then 27 cycles of 94° C. for 10 sec, 66° C.for 30 sec, 72° C. for 1.5 min. Five separate primary PCR reactions wereperformed for each experiment. The products were pooled and diluted 1:10with water. For the secondary PCR reaction, 1 μl from the pooled anddiluted primary PCR reaction was added to the same reaction mix as usedfor PCR 1, except that primers NP1 and NP2 (10 μM) were used instead ofPCR primer 1. PCR 2 was performed using 10-12 cycles of 94° C. for 10sec, 68° C. for 30 sec, and 72° C. for 1.5 minutes. The PCR productswere analyzed using 2% agarose gel electrophoresis.

[0439] The PCR products were inserted into pCR2.1 using the T/A vectorcloning kit (Invitrogen). Transformed E. coli were subjected toblue/white and ampicillin selection. White colonies were picked andarrayed into 96 well plates and were grown in liquid culture overnight.To identify inserts, PCR amplification was performed on 1 ml ofbacterial culture using the conditions of PCR1 and NP1 and NP2 asprimers. PCR products were analyzed using 2% agarose gelelectrophoresis.

[0440] Bacterial clones were stored in 20% glycerol in a 96 well format.Plasmid DNA was prepared, sequenced, and subjected to nucleic acidhomology searches of the GenBank, dBest, and NCI-CGAP databases.

[0441] RT-PCR Expression Analysis:

[0442] First strand cDNAs can be generated from 1 μg of mRNA with oligo(dT) 12-18 priming using the Gibco-BRL Superscript Preamplificationsystem. The manufacturer's protocol was used which included anincubation for 50 min at 42° C. with reverse transcriptase followed byRNAse H treatment at 37° C. for 20 min. After completing the reaction,the volume can be increased to 200 μl with water prior to normalization.First strand cDNAs from 16 different normal human tissues can beobtained from Clontech.

[0443] Normalization of the first strand cDNAs from multiple tissues wasperformed by using the primers 5′atatcgccgcgctcgtcgtcgacaa3′ (SEQ ID NO:714) and 5′agccacacgcagctcattgtagaagg 3′ (SEQ ID NO: 715) to amplifyβ-actin. First strand cDNA (5 μl) were amplified in a total volume of 50μl containing 0.4 μM primers, 0.2 μM each dNTPs, 1×PCR buffer (Clontech,10 mM Tris-HCL, 1.5 mM MgCl₂, 50 mM KCl, pH 8.3) and 1× Klentaq DNApolymerase (Clontech). Five μl of the PCR reaction can be removed at 18,20, and 22 cycles and used for agarose gel electrophoresis. PCR wasperformed using an MJ Research thermal cycler under the followingconditions: Initial denaturation can be at 94° C. for 15 sec, followedby a 18, 20, and 22 cycles of 94° C. for 15, 65° C. for 2 min, 72° C.for 5 sec. A final extension at 72° C. was carried out for 2 min. Afteragarose gel electrophoresis, the band intensities of the 283 b.p.β-actin bands from multiple tissues were compared by visual inspection.Dilution factors for the first strand cDNAs were calculated to result inequal β-actin band intensities in all tissues after 22 cycles of PCR.Three rounds of normalization can be required to achieve equal bandintensities in all tissues after 22 cycles of PCR.

[0444] To determine expression levels of the 213P1F11 gene, 5 μl ofnormalized first strand cDNA were analyzed by PCR using 26, and 30cycles of amplification. Semi-quantitative expression analysis can beachieved by comparing the PCR products at cycle numbers that give lightband intensities. The primers used for RT-PCR were designed using the213P1F11 SSH sequence and are listed below: 213P1F11.15′-GGATACCAGGGAACGCTTGGAG-3′ (SEQ ID NO:  ) 213P1F11.25′-TTTGACCTTTCCTGCTCAAGTAACC-3′ (SEQ ID NO:  )

[0445] A typical RT-PCR expression analysis is shown in FIG. 14. Firststrand cDNA was prepared from vital pool 1 (liver, lung and kidney),vital pool 2 (pancreas, colon and stomach), LAPC xenograft pool(LAPC-4AD, LAPC-4AI, LAPC-9AD and LAPC-9AI), bladder cancer pool, breastcancer pool, and cancer metastasis pool. Normalization was performed byPCR using primers to actin and GAPDH. Semi-quantitative PCR, usingprimers to 213P1F11, was performed at 26 and 30 cycles of amplification.Results show strong expression of 213P1F11 in bladder cancer pool,breast cancer pool, xenograft pool, and cancer metastasis pool, but notin the vital pools.

Example 2 Full Length Cloning of 213P1F11

[0446] The 213P1F11 SSH cDNA sequence was derived from a bladder cancerpool minus normal tissues cDNA subtraction. The SSH cDNA sequence(FIG. 1) was designated 213P1F1.

[0447] The SSH DNA sequence of 166 bp (FIG. 1) did not show homology toany known gene. The full-length cDNA 213P1F11 was cloned from bladdercancer cDNA. Variants of 213P1F11 were identified and these are listedin FIGS. 2 and 3. 213P1F11 v.1 reveals 100% identity to caspase-14precursor apoptosis-related cysteine protease protein (FIG. 4).

Example 3 Chromosomal Mapping of 213P1F11

[0448] Chromosomal localization can implicate genes in diseasepathogenesis. Several chromosome mapping approaches are availableincluding fluorescent in situ hybridization (FISH), human/hamsterradiation hybrid (RH) panels (Walter et al., 1994; Nature Genetics 7:22;Research Genetics, Huntsville Ala.), human-rodent somatic cell hybridpanels such as is available from the Coriell Institute (Camden, N.J.),and genomic viewers utilizing BLAST homologies to sequenced and mappedgenomic clones (NCBI, Bethesda, Md.).

[0449] 213P1F11 maps to chromosome 19p13.1 using 213P1F11 sequence andthe NCBI BLAST tool:(http:Hwww.ncbi.nlm.nih.gov/genome/seq/page.cgi?F-HsBlast.html&&ORG=Hs).

Example 4 Expression Analysis of 213P1F11 in Normal Tissues and PatientSpecimens

[0450] Expression analysis by RT-PCR demonstrated that 213P1F11 isstrongly expressed in bladder cancer patient specimens (FIG. 14). Firststrand cDNA was prepared from vital pool 1 (liver, lung and kidney),vital pool 2 (pancreas, colon and stomach), LAPC xenograft pool(LAPC-4AD, LAPC-4AI, LAPC-9AD and LAPC-9AI), bladder cancer pool, breastcancer pool, and cancer metastasis pool. Normalization was performed byPCR using primers to actin and GAPDH. Semi-quantitative PCR, usingprimers to 213P1F11, was performed at 26 and 30 cycles of amplification.Results show strong expression of 213P1F11 in bladder cancer pool,breast cancer pool, xenograft pool, and cancer metastasis pool, but notin the vital pools.

[0451] To determine the relative expression of 213P1F11 v.1 compared to213P1F11 v.2 in human cancers, primers were designed flanking theinsertion in 213P1F11 v.2 (FIG. 15). Using these primers, amplificationof 213P1F11 v.1 will generate a PCR fragment of 165 bp, whereas 213P1F11v.2 will generate a PCR fragment of 249 bp as depicted in FIG. 15. ThePCR product of 165 bp will also correspond to the variants 213P1F11 v.3,v.4, v.5, v.6 and v.7. First strand cDNA was prepared from vital pool 1(liver, lung and kidney), bladder cancer pool, breast cancer pool, LAPCxenograft pool (LAPC-4AD, LAPC-4AI, LAPC-9AD and LAPC-9AI), and 213P1F11v.1 plasmid control. Normalization was performed by PCR using primers toactin and GAPDH. Semi-quantitative PCR, using primers depicted above,was performed at 35 cycles of amplification. Results show strongexpression of 213P1F11 v.1 in bladder cancer pool, breast cancer pool,LAPC xenograft pool, and the plasmid positive control. A lowerexpression of the 249 bp 213P1F11 v.2 product was detected in breastcancer pool, LAPC xenograft pool, and to lower extent in bladder cancerpool. Altogether these data show that expression of 213P1F11 v.1 is moreabundant than 213P1F11 v.2 in human patient cancer samples.

[0452] Extensive northern blot analysis of 213P1F11 in multiple humannormal tissues is shown in FIG. 16. Strong expression was only detectedin skin tissue. A weak transcript is detected in normal thymus but notin the other tissues tested.

[0453] RNA was extracted from normal prostate, LAPC-4AD, LAPC-4AI,LAPC-9AD and LAPC-9AI prostate cancer xenografts. Northern blot with 10μg of total RNA/lane was probed with 213P1F11 SSH sequence (FIG. 18).Results show expression of 213P1F11 in the LAPC-9AI xenograft, but notin the other xenografts nor in normal prostate.

[0454] Expression of 213P1F11 in patient bladder cancer specimens isshown in FIG. 17. RNA was extracted from normal bladder (N), bladdercancer cell lines (UM-UC-3 and SCaBER), bladder cancer patient tumors(T) and normal tissue adjacent to bladder cancer (NAT). Northern blotswith 10 ug of total RNA were probed with the 213P1F11 SSH fragment. Sizestandards in kilobases are indicated on the side. Results show strongexpression of 213P1F11 in the bladder tumor tissues but not in normalbladder, nor in the bladder cancer cell lines.

[0455]FIG. 19 shows that 213P1F11 was expressed in breast cancer patienttissues. RNA was extracted from normal breast (N), breast cancer celllines (DU4475, MCF7 and CAMA-1), breast cancer patient tumors (T) andbreast cancer metastasis to lymph node (Met). Northern blots with 10 ugof total RNA were probed with the 213P1F11 SSH fragment. Results showstrong expression of 213P1F11 in the breast tumor tissues as well as inthe cancer metastasis specimen. Weak expression was also detected in theCAMA-1 cell line, but not in the other 2 breast cancer cell linestested.

[0456] The restricted expression of 213P1F11 in normal tissues and theexpression detected in bladder cancer, breast cancer, prostate cancerxenograft, and cancer metastases suggest that 213P1F11 is a potentialtherapeutic target and a diagnostic marker for human cancers.

Example 5 Transcript Variants of 213P1F11

[0457] Transcript variants are variants of matured mRNA from the samegene by alternative transcription or alternative splicing. Alternativetranscripts are transcripts from the same gene but start transcriptionat different points. Splice variants are mRNA variants spliceddifferently from the same transcript. In eukaryotes, when a multi-exongene is transcribed from genomic DNA, the initial RNA is spliced toproduce functional mRNA, which has only exons and is used fortranslation into an amino acid sequence. Accordingly, a given gene canhave zero to many alternative transcripts and each transcript can havezero to many splice variants. Each transcript variant has a unique exonmakeup, and can have different coding and/or non-coding (5′ or 3′ end)portions, from the original transcript. Transcript variants can code forsimilar or different proteins with the same or a similar function or mayencode proteins with different functions, and may be expressed in thesame tissue at the same time, or at different tissue, or at differenttimes, proteins encoded by transcript variants can have similar ordifferent cellular or extracellular localizations, i.e., be secreted.

[0458] Transcript variants are identified by a variety of art-acceptedmethods. For example, alternative transcripts and splice variants areidentified in a full-length cloning experiment, or by use of full-lengthtranscript and EST sequences. First, all human ESTs were grouped intoclusters which show direct or indirect identity with each other. Second,ESTs in the same cluster were further grouped into sub-clusters andassembled into a consensus sequence. The original gene sequence iscompared to the consensus sequence(s) or other full-length sequences.Each consensus sequence is a potential splice variant for that gene(see, e.g.,http://www.doubletwist.com/products/c11_agentsOverview.jhtml). Even whena variant is identified that is not a full-length clone, that portion ofthe variant is very useful for antigen generation and for furthercloning of the full-length splice variant, using techniques known in theart.

[0459] Moreover, computer programs are available in the art thatidentify transcript variants based on genomic sequences. Genomic-basedtranscript variant identification programs include FgenesH (A. Salamovand V. Solovyev, “Ab initio gene finding in Drosophila genomic DNA,”Genome Research. April 2000;10(4):516-22); Grail(http://compbio.oml.gov/Grail-bin/EmptyGrailForm) and GenScan(http://genes.mit.edu/GENSCAN.html). For a general discussion of splicevariant identification protocols see., e.g., Southan, C., A genomicperspective on human proteases, FEBS Lett. Jun. 8, 2001; 498(2-3):214-8;de Souza, S. J., et al., Identification of human chromosome 22transcribed sequences with ORF expressed sequence tags, Proc. Natl. AcadSci USA. Nov. 7, 2000; 97(23):12690-3.

[0460] To further confirm the parameters of a transcript variant, avariety of techniques are available in the art, such as full-lengthcloning, proteomic validation, PCR-based validation, and 5′ RACEvalidation, etc. (see e.g., Proteomic Validation: Brennan, S. O., et at,Albumin banks peninsula: a new termination variant characterized byelectrospray mass spectrometry, Biochem Biophys Acta. Aug. 17,1999;1433(1-2):321-6; Ferranti P, et al, Differential splicing ofpre-messenger RNA produces multiple forms of mature caprinealpha(sl)-casein, Eur J. Biochem. Oct. 1, 1997;249(1):1-7. For PCR-basedValidation: Wellmann S, et al., Specific reverse transcription-PCRquantification of vascular endothelial growth factor (VEGF) splicevariants by LightCycler technology, Clin Chem. April 2001;47(4):654-60;Jia, H. P., et al., Discovery of new human beta-defensins using agenomics-based approach, Gene. Jan. 24, 2001; 263(1-2):211-8. ForPCR-based and 5′ RACE Validation: Brigle, K. E., et at, Organization ofthe murine reduced folate carrier gene and identification of variantsplice forms, Biochem Biophys Acta. Aug. 7, 1997; 1353(2): 191-8).

[0461] It is known in the art that genomic regions are modulated incancers. When the genomic region, to which a gene maps, is modulated ina particular cancer, the alternative transcripts or splice variants ofthe gene are modulated as well. Disclosed herein is that 213P1 E 1 has aparticular expression profile related to cancer. Alternative transcriptsand splice variants of 213P F11 may also be involved in cancers in thesame or different tissues, thus serving as tumor-associatedmarkers/antigens.

[0462] The exon composition of the original transcript, designated as213P1F11 v.1, is shown in Table XXIIIA. Using the full-length gene andEST sequences, two splice variants were identified, designated as213P1F11 v.2 and 213P1F11 v.3. Compared with 213P1F11 v.1, splicevariant 213P1F11 v.2 had a longer exon 6 while 213P1F11 had a longerexon 5. Using the computer program GenScan, one alternative transcriptwas identified, designated as 213P1F11 v.4. This alternative transcripthad three different leading exons in place of the first two exons of213P1F11 v.1. The exon composition of the alternative transcript213P1F11 v.4 is shown in Table XXIIIB. Since 213P1F11 v.4 shares thesame exons 5 and 6 as 213P1F11 v.1, splice variants of this alternativetranscript with a longer exon 5 or a longer exon 6, or both, may existin human tissues. In fact, each different combination of exons inspatial order, e.g., exons 1, 2, 3, 4 and 7, is a potential splicevariant. FIG. 13 shows the schematic alignment of exons of the twotranscripts (in addition to variants 2 and 3).

[0463] Tables XXIV through XXVII are set forth herein on avariant-by-variant basis. Table XXIV shows the nucleotide sequences oftranscript variant 2 through variant 4. Table XXV shows the alignment oftranscript variant 2 through variant 4, each with the nucleic acidsequence of 213P1F11 variant 1. Table XXVI lays out amino acidtranslation of transcript variant 2 through variant 4 for the identifiedreading frame orientation. Table XXVII displays alignments of the aminoacid sequences encoded by splice variant 2 through variant 4, each withthat of 213P1F11 variant 1. Table XXVIII displays clustal alignments of213P1F11 protein variant 1 through variant 6.

Example 6 Single Nucleotide Polymorphisms of 213P1F11

[0464] Single Nucleotide Polymorphism (SNP) is a single base pairvariation in nucleotide sequences. At a specific point of the genome,there are four possible nucleotide base pairs: A/T, C/G, G/C and T/A.Genotype refers to the base pair make-up of one or more spots in thegenome of an individual, while haplotype refers to base pair make-up ofmore than one varied spots on the same DNA molecule (chromosome inhigher organism). SNPs that occur on a cDNA are called cSNPs. ThesecSNPs may change amino acids of the protein encoded by the gene and thuschange the functions of the protein. Some SNPs cause inherited diseasesand some others contribute to quantitative variations in phenotype andreactions to environmental factors including diet and drugs amongindividuals. Therefore, SNPs and/or combinations of alleles (calledhaplotypes) have many applications including diagnosis of inheriteddiseases, determination of drug reactions and dosage, identification ofgenes responsible for disearses and discovery of genetic relationshipbetween individuals (P. Nowotny, J. M. Kwon and A. M. Goate, “SNPanalysis to dissect human traits,” Curr. Opin. Neurobiol. October 2001;11(5):637-641; M. Pirmohamed and B. K. Park, “Genetic susceptibility toadverse drug reactions,” Trends Pharmacol. Sci. June 2001;22(6):298-305; J. H. Riley, C. J. Allan, E. Lai and A. Roses, “The useof single nucleotide polymorphisms in the isolation of common diseasegenes,” Pharmacogenomics. February 2000; 1(1):39-47; R. Judson, J. C.Stephens and A. Windemuth, “The predictive power of haplotypes inclinical response,” Pharmacogenomics. February 2000; 1(1):15-26).

[0465] SNPs are identified by a variety of art-accepted methods (P.Bean, “The promising voyage of SNP target discovery,” Am. Clin. Lab.October-November 2001; 20(9):18-20; K. M. Weiss, “In search of humanvariation,” Genome Res. July 1998; 8(7):691-697; M. M. She, “Enablinglarge-scale pharmacogenetic studies by high-throughput mutationdetection and genotyping technologies,” Clin. Chem. February 2001;47(2):164-172). For example, SNPs are identified by sequencing DNAfragments that show polymorphism by gel-based methods such asrestriction fragment length polymorphism (RFLP) and denaturing gradientgel electrophoresis (DGGE). They can also be discovered by directsequencing of DNA samples pooled from different individuals or bycomparing sequences from different DNA samples. With the rapidaccumulation of sequence data in public and private databases, one candiscover SNPs by comparing sequences using computer programs (Z. Gu, L.Hillier and P. Y. Kwok, “Single nucleotide polymorphism hunting incyberspace,” Hum. Mutat. 1998; 12(4):221-225). SNPs can be verified andgenotype or haplotype of an individual can be determined by a variety ofmethods including direct sequencing and high throughput microarrays (P.Y. Kwok, “Methods for genotyping single nucleotide polymorphisms,” Annu.Rev. Genomics Hum. Genet. 2001; 2:235-258; M. Kokoris, K. Dix, K.Moynihan, J. Mathis, B. Erwin, P. Grass, B. Hines and A. Duesterhoeft,“High-throughput SNP genotyping with the Masscode system,” Mol. Diagn.December 2000; 5(4):329-340).

[0466] Using the methods described above, six SNPs were identified inthe original transcript, 213P1F11 v.1, at positions 473 (T/C), 737(C/A), 2027 (C/T), 2037 (T/C), 2268 (A/G) and 3196 (A/T). Thetranscripts or proteins with alternative alleles were designated asvariants 213P1F11 v.5, v.6, v.7, v.8, v.9, and v.10. FIG. 10 shows theschematic alignment of the nucleotide variants. FIG. 11 shows theschematic alignment of protein variants, corresponding to nucleotidevariants. Nucleotide variants that code for the same amino acid sequenceas variant 1 are not shown in FIG. 11. These alleles of the SNPs, thoughshown separately here, can occur in different combinations (haplotypes)and in any one of the transcript variants that contains the sequencecontext of the SNPs, e.g., 213P1F11 v.2, 213P1F11 v.3 or 213P1f11 v.4.

Example 7 Production of Recombinant 213P1F11 in Prokaryotic Systems

[0467] To express recombinant 213P1F11 and 213P1F11 variants inprokaryotic cells, the full or partial length 213P1F11 and 213P1F11variant cDNA sequences are cloned into any one of a variety ofexpression vectors known in the art. One or more of the followingregions of 213P1F11 or 213P1F11 variants are expressed in theseconstructs, amino acids 1 to 242 of 213P1F11 variant 1, amino acids1-230 of variant 2, amino acids 1-146 of variant 3, amino acids 1-321 ofvariant 4; or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino acids from213P1F11, variants, or analogs thereof.

[0468] A. In vitro Transcription and Translation Constructs:

[0469] pCRII: To generate 213P1F11 sense and anti-sense RNA probes forRNA in situ investigations, pCRII constructs (Invitrogen, CarlsbadCalif.) are generated encoding either all or fragments of the 213P1F11cDNA. The pCRII vector has Sp6 and T7 promoters flanking the insert todrive the transcription of 213P1F11 RNA for use as probes in RNA in situhybridization experiments. These probes are used to analyze the cell andtissue expression of 213P1F11 at the RNA level. Transcribed 213P1F11 RNArepresenting the cDNA amino acid coding region of the 213P1F11 gene isused in in vitro translation systems such as the TnT™ CoupledReticulolysate Sytem (Promega, Corp., Madison, Wis.) to synthesize213P1F11 protein.

[0470] B. Bacterial Constructs:

[0471] pGEX Constructs: To generate recombinant 213P1F11 proteins inbacteria that are fused to the Glutathione S-transferase (GST) protein,all or parts of the T-fusion vector of the pGEX family (AmershamPharmacia Biotech, Piscataway, N.J.). These constructs allow controlledexpression of recombinant 213P1F11 protein sequences with GST fused atthe amino-terminus and a six histidine epitope (6×His) at thecarboxyl-terminus. The GST and 6×His tags permit purification of therecombinant fusion protein from induced bacteria with the appropriateaffinity matrix and allow recognition of the fusion protein withanti-GST and anti-His antibodies. The 6×His tag is generated by adding 6histidine codons to the cloning primer at the 3′ end, e.g., of the openreading frame (ORF). A proteolytic cleavage site, such as thePreScission™ recognition site in pGEX-6P-1, may be employed such that itpermits cleavage of the GST tag from 213P1F11-related protein. Theampicillin resistance gene and pBR322 origin permits selection andmaintenance of the pGEX plasmids in E. coli.

[0472] pMAL Constructs: To generate, in bacteria, recombinant 213P1F11proteins that are fused to maltose-binding protein (MBP), all or partsof the 213P1F11 cDNA protein coding sequence are fused to the MBP geneby cloning into the pMAL-c2X and pMAL-p2X vectors (New England Biolabs,Beverly, Mass.). These constructs allow controlled expression ofrecombinant 213P1F11 protein sequences with MBP fused at theamino-terminus and a 6×His epitope tag at the carboxyl-terminus. The MBPand 6×His tags permit purification of the recombinant protein frominduced bacteria with the appropriate affinity matrix and allowrecognition of the fusion protein with anti-MBP and anti-His antibodies.The 6×His epitope tag is generated by adding 6 histidine codons to the3′ cloning primer. A Factor Xa recognition site permits cleavage of thepMAL tag from 213P1F11. The pMAL-c2X and pMAL-p2X vectors are optimizedto express the recombinant protein in the cytoplasm or periplasmrespectively. Periplasm expression enhances folding of proteins withdisulfide bonds.

[0473] pET Constructs: To express 213P1F11 in bacterial cells, all orparts of the 213P1F11 cDNA protein coding sequence are cloned into thepET family of vectors (Novagen, Madison, Wis.). These vectors allowtightly controlled expression of recombinant 213P1F11 protein inbacteria with and without fusion to proteins that enhance solubility,such as NusA and thioredoxin (Trx), and epitope tags, such as 6×His andS-Tag™ that aid purification and detection of the recombinant protein.For example, constructs are made utilizing pET NusA fusion system 43.1such that regions of the 213P1F11 protein are expressed asamino-terminal fusions to NusA.

[0474] C. Yeast Constructs:

[0475] pESC Constructs: To express 213P1F11 in the yeast speciesSaccharomyces cerevisiae for generation of recombinant protein andfunctional studies, all or parts of the 213P1F11 cDNA protein codingsequence are cloned into the pESC family of vectors each of whichcontain 1 of 4 selectable markers, HIS3, TRP 1, LEU2, and URA3(Stratagene, La Jolla, Calif.). These vectors allow controlledexpression from the same plasmid of up to 2 different genes or clonedsequences containing either Flag™ or Myc epitope tags in the same yeastcell. This system is useful to confirm protein-protein interactions of213P1F11. In addition, expression in yeast yields similarpost-translational modifications, such as glycosylations andphosphorylations, that are found when expressed in eukaryotic cells.

[0476] pESP Constructs: To express 213P1F11 in the yeast speciesSaccharomyces pombe, all or parts of the 213P1F11 cDNA protein codingsequence are cloned into the pESP family of vectors. These vectors allowcontrolled high level of expression of a 213P1F11 protein sequence thatis fused at either the amino terminus or at the carboxyl terminus to GSTwhich aids purification of the recombinant protein. A Flag™ epitope tagallows detection of the recombinant protein with anti-Flag™ antibody.

Example 8 Production of Recombinant 213P1F11 in Eukaryotic Systems A.Mammalian Constructs:

[0477] To express recombinant 213P1F11 in eukaryotic cells, the full orpartial length 213P1F11 cDNA sequences can be cloned into any one of avariety of expression vectors known in the art. One or more of thefollowing regions of 213P1F11 are expressed in these constructs, aminoacids 1 to 242, or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino acidsfrom 213P1F11, variants, or analogs thereof. In certain embodiments aregion of a specific variant of 213P1F11 is expressed that encodes anamino acid at a specific position which differs from the amino acid ofany other variant found at that position. In other embodiments, a regionof a variant of 213P1F11 is expressed that lies partly or entirelywithin a sequence that is unique to that variant.

[0478] The constructs can be transfected into any one of a wide varietyof mammalian cells such as 293T cells. Transfected 293T cell lysates canbe probed with the anti-213P1F11 polyclonal serum, described herein.

[0479] pcDNA4/HisMax Constructs: To express 213P1F11 in mammalian cells,a 213P1F11 ORF, or portions thereof, of 213P1F11 are cloned intopcDNA4/HisMax Version A (Invitrogen, Carlsbad, Calif.). Proteinexpression is driven from the cytomegalovirus (CMV) promoter and the SP16 translational enhancer. The recombinant protein has Xpress™ and sixhistidine (6×His) epitopes fused to the amino-terminus. ThepcDNA4/HisMax vector also contains the bovine growth hormone (BGH)polyadenylation signal and transcription termination sequence to enhancemRNA stability along with the SV40 origin for episomal replication andsimple vector rescue in cell lines expressing the large T antigen. TheZeocin resistance gene allows for selection of mammalian cellsexpressing the protein and the ampicillin resistance gene and ColE1origin permits selection and maintenance of the plasmid in E. coli.

[0480] pcDNA3.1/MycHis Constructs: To express 213P1F11 in mammaliancells, a 213P1F11 ORF, or portions thereof, of 213P1F11 with a consensusKozak translation initiation site are cloned into pcDNA3.1/MycHisVersion A (Invitrogen, Carlsbad, Calif.). Protein expression is drivenfrom the cytomegalovirus (CMV) promoter. The recombinant proteins havethe myc epitope and 6×His epitope fused to the carboxyl-terminus. ThepcDNA3.1/MycHis vector also contains the bovine growth hormone (BGH)polyadenylation signal and transcription termination sequence to enhancemRNA stability, along with the SV40 origin for episomal replication andsimple vector rescue in cell lines expressing the large T antigen. TheNeomycin resistance gene can be used, as it allows for selection ofmammalian cells expressing the protein and the ampicillin resistancegene and ColE1 origin permits selection and maintenance of the plasmidin E. coli.

[0481] pcDNA3.1/CT-GFP-TOPO Construct: To express 213P1F11 in mammaliancells and to allow detection of the recombinant proteins usingfluorescence, a 213P1F11 ORF, or portions thereof, with a consensusKozak translation initiation site are cloned into pcDNA3.1/CT-GFP-TOPO(Invitrogen, Calif.). Protein expression is driven from thecytomegalovirus (CMV) promoter. The recombinant proteins have the GreenFluorescent Protein (GFP) fused to the carboxyl-terminus facilitatingnon-invasive, in vivo detection and cell biology studies. The pcDNA3.1CT-GFP-TOPO vector also contains the bovine growth hormone (BGH)polyadenylation signal and transcription termination sequence to enhancemRNA stability along with the SV40 origin for episomal replication andsimple vector rescue in cell lines expressing the large T antigen. TheNeomycin resistance gene allows for selection of mammalian cells thatexpress the protein, and the ampicillin resistance gene and ColE1 originpermits selection and maintenance of the plasmid in E. coli. Additionalconstructs with an amino-terminal GFP fusion are made inpcDNA3.1/NT-GFP-TOPO spanning the entire length of a 213P1F11 protein.

[0482] PAPtag: A 213P1F11 ORF, or portions thereof, is cloned intopAPtag-5 (GenHunter Corp. Nashville, Tenn.). This construct generates analkaline phosphatase fusion at the carboxyl-terminus of a 213P1F11protein while fusing the IgGκ signal sequence to the amino-terminus.Constructs are also generated in which alkaline phosphatase with anamino-terminal IgGκ signal sequence is fused to the amino-terminus of a213P1F11 protein. The resulting recombinant 213P1F11 proteins areoptimized for secretion into the media of transfected mammalian cellsand can be used to identify proteins such as ligands or receptors thatinteract with 213P1F11 proteins. Protein expression is driven from theCMV promoter and the recombinant proteins also contain myc and 6×Hisepitopes fused at the carboxyl-terminus that facilitates detection andpurification. The Zeocin resistance gene present in the vector allowsfor selection of mammalian cells expressing the recombinant protein andthe ampicillin resistance gene permits selection of the plasmid in E.coli.

[0483] ptag5: A 213P1F11 ORF, or portions thereof, is cloned intopTag-5. This vector is similar to pAPtag but without the alkalinephosphatase fusion. This construct generates 213P1F11 protein with anamino-terminal IgGK signal sequence and myc and 6×His epitope tags atthe carboxyl-terminus that facilitate detection and affinitypurification. The resulting recombinant 213P1F11 protein is optimizedfor secretion into the media of transfected mammalian cells, and is usedas immunogen or ligand to identify proteins such as ligands or receptorsthat interact with the 213P1F11 proteins. Protein expression is drivenfrom the CMV promoter. The Zeocin resistance gene present in the vectorallows for selection of mammalian cells expressing the protein, and theampicillin resistance gene permits selection of the plasmid in E. coli.

[0484] PsecFc: A 213P1F11 ORF, or portions thereof, is also cloned intopsecFc. The psecFc vector was assembled by cloning the humanimmunoglobulin G1 (IgG) Fc (hinge, CH2, CH3 regions) into pSecTag2(Invitrogen, Calif.). This construct generates an IgG1 Fc fusion at thecarboxyl-terminus of the 213P1F11 proteins, while fusing the IgGK signalsequence to N-terminus. 213P1F11 fusions utilizing the murine IgG1 Fcregion are also used. The resulting recombinant 213P1F11 proteins areoptimized for secretion into the media of transfected mammalian cells,and can be used as immunogens or to identify proteins such as ligands orreceptors that interact with 213P1F11 protein. Protein expression isdriven from the CMV promoter. The hygromycin resistance gene present inthe vector allows for selection of mammalian cells that express therecombinant protein, and the ampicillin resistance gene permitsselection of the plasmid in E. coli.

[0485] pSRαConstructs: To generate mammalian cell lines that express213P1F11 constitutively, 213P1F11 ORF, or portions thereof, of 213P1F11are cloned into pSRα constructs. Amphotropic and ecotropic retrovirusesare generated by transfection of pSRα constructs into the 293T-10A1packaging line or co-transfection of pSRα and a helper plasmid(containing deleted packaging sequences) into the 293 cells,respectively. The retrovirus is used to infect a variety of mammaliancell lines, resulting in the integration of the cloned gene, 213P1F11,into the host cell-lines. Protein expression is driven from a longterminal repeat (LTR). The Neomycin resistance gene present in thevector allows for selection of mammalian cells that express the protein,and the ampicillin resistance gene and ColE 1 origin permit selectionand maintenance of the plasmid in E. coli. The retroviral vectors canthereafter be used for infection and generation of various cell linesusing, for example, PC3, NIH 3T3, TsuPr1, 293 or rat-i cells.

[0486] Additional pSRc constructs are made that fuse an epitope tag suchas the FLAG™ tag to the carboxyl-terminus of 213P1F11 sequences to allowdetection using anti-Flag antibodies. For example, the FLAG™ sequence 5′gat tac aag gat gac gac gat aag 3′ (SEQ ID NO:______) is added tocloning primer at the 3′ end of the ORF. Additional pSRox constructs aremade to produce both amino-terminal and carboxyl-terminal GFP andmyc/6×His fusion proteins of the full-length 213P1F11 proteins.

[0487] Additional Viral Vectors: Additional constructs are made forviral-mediated delivery and expression of 213P1F11. High virus titerleading to high level expression of 213P1F11 is achieved in viraldelivery systems such as adenoviral vectors and herpes amplicon vectors.A 213P1F11 coding sequences or fragments thereof are amplified by PCRand subcloned into the AdEasy shuttle vector (Stratagene). Recombinationand virus packaging are performed according to the manufacturer'sinstructions to generate adenoviral vectors. Alternatively, 213P1F11coding sequences or fragments thereof are cloned into the HSV-1 vector(Imgenex) to generate herpes viral vectors. The viral vectors arethereafter used for infection of various cell lines such as PC3, NIH3T3, 293 or rat-1 cells.

[0488] Regulated Expression Systems: To control expression of 213P1F11in mammalian cells, coding sequences of 213P1F11, or portions thereof,are cloned into regulated mammalian expression systems such as the T-RexSystem (Invitrogen), the GeneSwitch System (Invitrogen) and thetightly-regulated Ecdysone System (Sratagene). These systems allow thestudy of the temporal and concentration dependent effects of recombinant213P1F11. These vectors are thereafter used to control expression of213P1F11 in various cell lines such as PC3, NIH 3T3, 293 or rat-1 cells.

[0489] B. Baculovirus Expression Systems

[0490] To generate recombinant 213P1F11 proteins in a baculovirusexpression system, 213P1F11 ORF, or portions thereof, are cloned intothe baculovirus transfer vector pBlueBac 4.5 (Invitrogen), whichprovides a His-tag at the N-terminus. Specifically, pBlueBac-213P1F11 isco-transfected with helper plasmid pBac-N-Blue (Invitrogen) into SF9(Spodoptera frugiperda) insect cells to generate recombinant baculovirus(see Invitrogen instruction manual for details). Baculovirus is thencollected from cell supernatant and purified by plaque assay.

[0491] Recombinant 213P1F11 protein is then generated by infection ofHighFive insect cells (Invitrogen) with purified baculovirus.Recombinant 213P1F11 protein can be detected using anti-213P1F11 oranti-His-tag antibody. 213P1F11 protein can be purified and used invarious cell-based assays or as immunogen to generate polyclonal andmonoclonal antibodies specific for 213P1F11.

Example 9 Antigenicity Profiles and Secondary Structure

[0492] FIGS. 5A-D, FIGS. 6A-D, FIGS. 7A-D, FIGS. 8A-D, and FIGS. 9A-Ddepict graphically five amino acid profiles of the 213P1F11 variants 1through 4 respectively, each assessment available by accessing theProtScale website (URL www.expasy.ch/cgi-bin/protscale.pl) on the ExPasymolecular biology server.

[0493] These profiles: FIG. 5, Hydrophilicity, (Hopp T. P., Woods K. R.,1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828); FIG. 6,Hydropathicity, (Kyte J., Doolittle R. F., 1982. J. Mol. Biol.157:105-132); FIG. 7, Percentage Accessible Residues (Janin J., 1979Nature 277:491-492); FIG. 8, Average Flexibility, (Bhaskaran R., andPonnuswamy P. K., 1988. Int. J. Pept. Protein Res. 32:242-255); FIG. 9,Beta-turn (Deleage, G., Roux B. 1987 Protein Engineering 1:289-294); andoptionally others available in the art, such as on the ProtScalewebsite, were used to identify antigenic regions of the 213P1F11protein. Each of the above amino acid profiles of 213P1F11 weregenerated using the following ProtScale parameters for analysis: 1) Awindow size of 9; 2) 100% weight of the window edges compared to thewindow center; and, 3) amino acid profile values normalized to liebetween 0 and 1.

[0494] Hydrophilicity (FIG. 5), Hydropathicity (FIG. 6) and PercentageAccessible Residues (FIG. 7) profiles were used to determine stretchesof hydrophilic amino acids (i.e., values greater than 0.5 on theHydrophilicity and Percentage Accessible Residues profile, and valuesless than 0.5 on the Hydropathicity profile). Such regions are likely tobe exposed to the aqueous environment, be present on the surface of theprotein, and thus available for immune recognition, such as byantibodies.

[0495] Average Flexibility (FIG. 8) and Beta-turn (FIG. 9) profilesdetermine stretches of amino acids (i.e., values greater than 0.5 on theBeta-turn profile and the Average Flexibility profile) that are notconstrained in secondary structures such as beta sheets and alphahelices. Such regions are also more likely to be exposed on the proteinand thus accessible to immune recognition, such as by antibodies.

[0496] Antigenic sequences of the 213P1F11 protein and of the variantproteins indicated, e.g., by the profiles set forth in FIGS. 5A-D, FIGS.6A-D, FIGS. 7A-D, FIGS. 8A-D, and/or FIGS. 9A-D are used to prepareimmunogens, either peptides or nucleic acids that encode them, togenerate therapeutic and diagnostic anti-213P1F11 antibodies. Theimmunogen can be any 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50 or more than 50contiguous amino acids, or the corresponding nucleic acids that encodethem, from the 213P1F11 protein variants listed in FIGS. 2 and 3. Inparticular, peptide immunogens of the invention can comprise, a peptideregion of at least 5 amino acids of FIGS. 2 and 3 in any whole numberincrement up to the full length of the respective variant's sequencethat includes an amino acid position having a value greater than 0.5 inthe Hydrophilicity profiles of FIGS. 5A-D; a peptide region of at least5 amino acids of FIGS. 2 and 3 in any whole number increment up to thefull length of the respective variant's sequence that includes an aminoacid position having a value less than 0.5 in the Hydropathicity profileof FIGS. 6A-D; a peptide region of at least 5 amino acids of FIGS. 2 and3 in any whole number increment up to the full length of the respectivevariant's sequence that includes an amino acid position having a valuegreater than 0.5 in the Percent Accessible Residues profiles of FIGS.7A-D; a peptide region of at least 5 amino acids of FIGS. 2 and 3 in anywhole number increment up to the full length of the respective variant'ssequence that includes an amino acid position having a value greaterthan 0.5 in the Average Flexibility profiles on FIGS. 8A-D; and, apeptide region of at least 5 amino acids of FIGS. 2 and 3 in any wholenumber increment up to the full length of the respective variant'ssequence that includes an amino acid position having a value greaterthan 0.5 in the Beta-turn profile of FIGS. 9A-D. Peptide immunogens ofthe invention can also comprise nucleic acids that encode any of theforgoing.

[0497] All immunogens of the invention, peptide or nucleic acid, can beembodied in human unit dose form, or comprised by a composition thatincludes a pharmaceutical excipient compatible with human physiology.

[0498] The secondary structures of 213P1F11 variants 1 through 4, namelythe predicted presence and location of alpha helices, extended strands,and random coils, are predicted from the primary amino acid sequenceusing the HNN—Hierarchical Neural Network method (Guermeur, 1997,http://pbil.ibcp.fr/cgi-bin/npsa_automat.p1?pagemnpsa_nn.html), accessedfrom the ExPasy molecular biology server (http://www.expasy.ch/tools/).The analysis indicates that 213P1F11 variant 1 is composed 47.93% alphahelix, 11.57% extended strand, and 40.50% random coil (FIG. 12A),variant 2 is composed of 38.70% alpha helix, 9.57% extended strand, and51.74% random coil (FIG. 12B), variant 3 is composed of 50.68% alphahelix, 6.85% extended strand, and 42.47% random coil (FIG. 12C), andvariant 4 is composed of 39.25% alpha helix, 12.15% extended strand, and48.60% random coil (FIG. 12D).

[0499] Analysis for the potential presence of transmembrane domains in213P1F11 variant 1 was carried out using a variety of transmembraneprediction algorithms accessed from the ExPasy molecular biology server(http://www.expasy.ch/tools/) (Table XXII). The programs do not predictthe presence of transmembrane domains in any of the 213P1F11 variants,suggesting that each is a soluble protein.

Example 10 Generation of 213P1F11 Polyclonal Antibodies

[0500] Polyclonal antibodies can be raised in a mammal, for example, byone or more injections of an immunizing agent and, if desired, anadjuvant. Typically, the immunizing agent and/or adjuvant will beinjected in the mammal by multiple subcutaneous or intraperitonealinjections. In addition to immunizing with the full length 213P1F11protein, computer algorithms are employed in design of immunogens that,based on amino acid sequence analysis contain characteristics of beingantigenic and available for recognition by the immune system of theimmunized host (see the Example entitled “Antigenicity Profiles andSecondary Structure”). Such regions would be predicted to behydrophilic, flexible, in beta-turn conformations, and be exposed on thesurface of the protein (see, e.g., FIGS. 5A-D, FIGS. 6A-D, FIGS. 7A-D,FIGS. 8A-D, or FIGS. 9A-D for amino acid profiles that indicate suchregions of 213P1F11 and variants).

[0501] For example, 213P1F11 recombinant bacterial fusion proteins orpeptides containing hydrophilic, flexible, beta-turn regions of 213P1F11variant proteins are used as antigens to generate polyclonal antibodiesin New Zealand White rabbits. For example, such regions include, but arenot limited to, amino acids 1-17, amino acids 25-80, amino acids 88-108,amino acids 131-147, and 207-242 of 213P1F11 variant 1. It is useful toconjugate the immunizing agent to a protein known to be immunogenic inthe mammal being immunized. Examples of such immunogenic proteinsinclude, but are not limited to, keyhole limpet hemocyanin (KLH), serumalbumin, bovine thyroglobulin, and soybean trypsin inhibitor. In oneembodiment, a peptide encoding amino acids 1-17 of 213P1F11 variant 1 isconjugated to KLH and used to immunize the rabbit. Alternatively theimmunizing agent may include all or portions of the 213P1F11 variantproteins, analogs or fusion proteins thereof. For example, the 213P1F11variant 1 amino acid sequence can be fused using recombinant DNAtechniques to any one of a variety of fusion protein partners that arewell known in the art, such as glutathione-S-transferase (GST) and HIStagged fusion proteins. Such fusion proteins are purified from inducedbacteria using the appropriate affinity matrix.

[0502] In one embodiment, a GST-fusion protein encoding amino acids1-147, encompassing several predicted antigenic regions, is produced andpurified and used as immunogen. Other recombinant bacterial fusionproteins that may be employed include maltose binding protein, LacZ,thioredoxin, NusA, or an immunoglobulin constant region (see the sectionentitled “Production of 213P1F11 in Prokaryotic Systems” and CurrentProtocols In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubulet al. eds., 1995; Linsley, P. S., Brady, W., Umes, M., Grosmaire, L.,Damle, N., and Ledbetter, L. (1991) J. Exp. Med. 174, 561-566).

[0503] In addition to bacterial derived fusion proteins, mammalianexpressed protein antigens are also used. These antigens are expressedfrom mammalian expression vectors such as the Tag5 and Fc-fusion vectors(see the section entitled “Production of Recombinant 213P1F11 inEukaryotic Systems”), and retain post-translational modifications suchas glycosylations found in native protein. In one embodiment, the fulllength sequence of variant 1, amino acids 1-242, is cloned into the Tag5mammalian secretion vector. The recombinant protein is purified by metalchelate chromatography from tissue culture supernatants of 293T cellsstably expressing the recombinant vector. The purified Tag5 213P1F11protein is then used as immunogen.

[0504] During the immunization protocol, it is useful to mix or emulsifythe antigen in adjuvants that enhance the immune response of the hostanimal. Examples of adjuvants include, but are not limited to, completeFreund's adjuvant (CFA) and MPL-TDM adjuvant (monophosphoryl Lipid A,synthetic trehalose dicorynomycolate).

[0505] In a typical protocol, rabbits are initially immunizedsubcutaneously with up to 200 μg, typically 100-200 μg, of fusionprotein or peptide conjugated to KLH mixed in complete Freund's adjuvant(CFA). Rabbits are then injected subcutaneously every two weeks with upto 200 μg, typically 100-200 μg, of the immunogen in incomplete Freund'sadjuvant (IFA). Test bleeds are taken approximately 7-10 days followingeach immunization and used to monitor the titer of the antiserum byELISA.

[0506] To test reactivity and specificity of immune serum, such as therabbit serum derived from immunization with a KLH-conjugated peptideencoding amino acids 1-17 of variant 1, the full-length 213P11 variant 1cDNA is cloned into pcDNA 3.1 myc-his expression vector (Invitrogen, seethe Example entitled “Production of Recombinant 213P1F11 in EukaryoticSystems”). After transfection of the constructs into 293T cells, celllysates are probed with the anti-213P1P11 serum and with anti-Hisantibody (Santa Cruz Biotechnologies, Santa Cruz, Calif.) to determinespecific reactivity to denatured 213P1F11 protein using the Western blottechnique. The immune serum is then tested by the Western blot techniqueagainst 293T-213P1F11 cells. In addition, the immune serum is tested byfluorescence microscopy, flow cytometry and immunoprecipitation against293T and other recombinant 213P1F11-expressing cells to determinespecific recognition of native protein. Western blot,immunoprecipitation, fluorescent microscopy, and flow cytometrictechniques using cells that endogenously express 213P1F11 are alsocarried out to test reactivity and specificity.

[0507] Anti-serum from rabbits immunized with 213P1F11 variant fusionproteins, such as GST and MBP fusion proteins, are purified by depletionof antibodies reactive to the fusion partner sequence by passage over anaffinity column containing the fusion partner either alone or in thecontext of an irrelevant fusion protein. For example, antiserum derivedfrom a GST-213P1F11 fusion protein encoding amino acids 1-147 is firstpurified by passage over a column of GST protein covalently coupled toAffiGel matrix (BioRad, Hercules, Calif.). The antiserum is thenaffinity purified by passage over a column composed of a MBP-fusionprotein also encoding amino acids 1-147 covalently coupled to Affigelmatrix. The serum is then further purified by protein G affinitychromatography to isolate the IgG fraction. Sera from other His-taggedantigens and peptide immunized rabbits as well as fusion partnerdepleted sera are affinity purified by passage over a column matrixcomposed of the original protein immunogen or free peptide.

Example 11 Generation of 213P1F11 Monoclonal Antibodies (mAbs)

[0508] In one embodiment, therapeutic mAbs to 213P1F11 variants comprisethose that react with epitopes specific for each variant protein orspecific to sequences in common between the variants that would disruptor modulate the biological function of the 213P1F11 variants, forexample those that would disrupt the interaction with ligands andbinding partners. Immunogens for generation of such mAbs include thosedesigned to encode or contain the entire 213P1F11 protein variantsequence, regions of the 213P1F11 protein variants predicted to beantigenic from computer analysis of the amino acid sequence (see, e.g.,FIGS. 5A-D, FIGS. 6A-D, FIGS. 7A-D, FIGS. 8A-D, or FIGS. 9A-D, and theExample entitled “Antigenicity Profiles and Secondary Structure”).Immunogens include peptides, recombinant bacterial proteins, andmammalian expressed Tag 5 proteins and human and murine IgG FC fusionproteins. In addition, cells engineered to express high levels of arespective 213P1F11 variant, such as 293T-213P1F11 variant 1 or300.19-213P1F11 variant 1 murine Pre-B cells, are used to immunize mice.

[0509] To generate mAbs to a 213P1F11 variant, mice are first immunizedintraperitoneally (IP) with, typically, 10-50 μg of protein immunogen or10⁷ 213P1F11-expressing cells mixed in complete Freund's adjuvant. Miceare then subsequently immunized IP every 2-4 weeks with, typically,10-50 μg of protein immunogen or 10⁷ cells mixed in incomplete Freund'sadjuvant. Alternatively, MPL-TDM adjuvant is used in immunizations. Inaddition to the above protein and cell-based immunization strategies, aDNA-based immunization protocol is employed in which a mammalianexpression vector encoding a 213P1F11 variant sequence is used toimmunize mice by direct injection of the plasmid DNA. For example, thefull length variant I sequence, encoding amino acids 1-242, is clonedinto the Tag5 mammalian secretion vector and the recombinant vector isused as immunogen. In another example the same amino acids are clonedinto an Fc-fusion secretion vector in which the 213P1F11 variant Isequence is fused at the amino-terminus to an IgK leader sequence and atthe carboxyl-terminus to the coding sequence of the human or murine IgGFc region. This recombinant vector is then used as immunogen. Theplasmid immunization protocols are used in combination with purifiedproteins expressed from the same vector and with cells expressing therespective 213P1F11 variant.

[0510] During the immunization protocol, test bleeds are taken 7-10 daysfollowing an injection to monitor titer and specificity of the immuneresponse. Once appropriate reactivity and specificity is obtained asdetermined by ELISA, Western blotting, immunoprecipitation, fluorescencemicroscopy, and flow cytometric analyses, fusion and hybridomageneration is then carried out with established procedures well known inthe art (see, e.g., Harlow and Lane, 1988).

[0511] In one embodiment for generating 213P1F11 monoclonal antibodies,a Tag5-213P1F11 variant 1 antigen encoding amino acids 1-242, isexpressed and purified from stably transfected 293T cells. Balb C miceare initially immunized intraperitoneally with 25 μg of theTag5-213P1F11 variant 1 protein mixed in complete Freund's adjuvant.Mice are subsequently immunized every two weeks with 25 μg of theantigen mixed in incomplete Freund's adjuvant for a total of threeimmunizations. ELISA using the Tag5 antigen determines the titer ofserum from immunized mice. Reactivity and specificity of serum to fulllength 213P1F11 variant protein is monitored by Western blotting,immunoprecipitation and flow cytometry using 293T cells transfected withan expression vector encoding the 213P1F11 variant 1 cDNA (see e.g., theExample entitled “Production of Recombinant 213P1F11 in EukaryoticSystems”). Other recombinant 213P1F11 variant 1-expressing cells orcells endogenously expressing 213P1F11 variant 1 are also used. Miceshowing the strongest reactivity are rested and given a final injectionof Tag5 antigen in PBS and then sacrificed four days later. The spleensof the sacrificed mice are harvested and fused to SPO/2 myeloma cellsusing standard procedures (Harlow and Lane, 1988). Supernatants from HATselected growth wells are screened by ELISA, Western blot,immunoprecipitation, fluorescent microscopy, and flow cytometry toidentify 213P1F11 specific antibody-producing clones.

[0512] Monoclonal antibodies are also derived that react only withspecific 213P1F11 variants. To this end, immunogens are designed toencode amino acid regions specific to the respective variant. Forexample, a Tag5 immunogen encoding amino acids 175-230 of variant 2 isproduced, purified, and used to immunize mice to generate hybridomas. Inanother example, a KLH-coupled peptide encoding amino acids 135-146 ofvariant 3 is produced and used as immunogen. In another example aminoacids 1-86 of variant 4 is fused to GST and used as immunogen.Monoclonal antibodies raised to these immunogens are then screened forreactivity to cells expressing the respective variants but not to other213P1F11 variants. These strategies for raising 213P1F11 variantspecific monoclonal antibodies are also applied to polyclonal reagentsdescribed in the Example entitled “Generation of 213P1F11 PolyclonalAntibodies.”

[0513] The binding affinity of a 213P1F11 monoclonal antibody isdetermined using standard technologies. Affinity measurements quantifythe strength of antibody to epitope binding and are used to help definewhich 213P1F11 monoclonal antibodies preferred for diagnostic ortherapeutic use, as appreciated by one of skill in the art. The BIAcoresystem (Uppsala, Sweden) is a preferred method for determining bindingaffinity. The BIAcore system uses surface plasmon resonance (SPR,Welford K. 1991, Opt. Quant. Elect. 23: 1; Morton and Myszka, 1998,Methods in Enzymology 295: 268) to monitor biomolecular interactions inreal time. BIAcore analysis conveniently generates association rateconstants, dissociation rate constants, equilibrium dissociationconstants, and affinity constants.

Example 12 HLA Class I and Class II Binding Assays

[0514] HLA class I and class II binding assays using purified HLAmolecules are performed in accordance with disclosed protocols (e.g.,PCT publications WO 94/20127 and WO 94/03205; Sidney et al, CurrentProtocols in Immunology 18.3.1 (1998); Sidney, et al, J. Immunol.154:247 (1995); Sette, et al, Mol Immunol 31:813 (1994)). Briefly,purified MHC molecules (5 to 500 nM) are incubated with variousunlabeled peptide inhibitors and 1-10 nM ¹²⁵I-radiolabeled probepeptides as described. Following incubation, MHC-peptide complexes areseparated from free peptide by gel filtration and the fraction ofpeptide bound is determined. Typically, in preliminary experiments, eachMHC preparation is titered in the presence of fixed amounts ofradiolabeled peptides to determine the concentration of HLA moleculesnecessary to bind 10-20% of the total radioactivity. All subsequentinhibition and direct binding assays are performed using these HLAconcentrations.

[0515] Since under these conditions [label]<[HLA] and IC₅₀≧[HLA], themeasured IC₅₀ values are reasonable approximations of the true K_(D)values. Peptide inhibitors are typically tested at concentrationsranging from 120 μg/ml to 1.2 ng/ml, and are tested in two to fourcompletely independent experiments. To allow comparison of the dataobtained in different experiments, a relative binding figure iscalculated for each peptide by dividing the IC₅₀ of a positive controlfor inhibition by the IC₅₀ for each tested peptide (typically unlabeledversions of the radiolabeled probe peptide). For database purposes, andinter-experiment comparisons, relative binding values are compiled.These values can subsequently be converted back into IC₅₀ nM values bydividing the IC₅₀ nM of the positive controls for inhibition by therelative binding of the peptide of interest. This method of datacompilation is accurate and consistent for comparing peptides that havebeen tested on different days, or with different lots of purified MHC.

[0516] Binding assays as outlined above may be used to analyze HLAsupermotif and/or HLA motif-bearing peptides.

Example 13 Identification of HLA Supermotif- and Motif-Bearing CTLCandidate Epitopes

[0517] HLA vaccine compositions of the invention can include multipleepitopes. The multiple epitopes can comprise multiple HLA supermotifs ormotifs to achieve broad population coverage. This example illustratesthe identification and confirmation of supermotif- and motif-bearingepitopes for the inclusion in such a vaccine composition. Calculation ofpopulation coverage is performed using the strategy described below.

[0518] Computer Searches and Algorithms for Identification of Supermotifand/or Motif-Bearing Epitopes

[0519] The searches performed to identify the motif-bearing peptidesequences in the Example entitled “Antigenicity Profiles and SecondaryStructure” and Tables V-XIX employ the protein sequence data from thegene product of 213P1F11 set forth in FIGS. 2 and 3. ***THIS IS A PLACEWHERE WE CAN REFERENCE NEW SEARCH FRAGMENT TABLE***,

[0520] Computer searches for epitopes bearing HLA Class I or Class IIsupermotifs or motifs are performed as follows. All translated 213P1F11protein sequences are analyzed using a text string search softwareprogram to identify potential peptide sequences containing appropriateHLA binding motifs; such programs are readily produced in accordancewith information in the art in view of known motif/supermotifdisclosures. Furthermore, such calculations can be made mentally.

[0521] Identified A2-, A3-, and DR-supermotif sequences are scored usingpolynomial algorithms to predict their capacity to bind to specificHLA-Class I or Class II molecules. These polynomial algorithms accountfor the impact of different amino acids at different positions, and areessentially based on the premise that the overall affinity (or ΔG) ofpeptide-HLA molecule interactions can be approximated as a linearpolynomial function of the type:

[0522] “ΔG”=a_(1t)×a_(2t)×a_(3t) . . . ×a_(nt)

[0523] where a_(jt) is a coefficient which represents the effect of thepresence of a given amino acid (U) at a given position (i) along thesequence of a peptide of n amino acids. The crucial assumption of thismethod is that the effects at each position are essentially independentof each other (i.e., independent binding of individual side-chains).When residue j occurs at position i in the peptide, it is assumed tocontribute a constant amount j, to the free energy of binding of thepeptide irrespective of the sequence of the rest of the peptide.

[0524] The method of derivation of specific algorithm coefficients hasbeen described in Gulukota et al., J. Mol. Biol. 267:1258-126, 1997;(see also Sidney et al., Human Immunol. 45:79-93, 1996; and Southwood etal, J. Immunol. 160:3363-3373, 1998). Briefly, for all i positions,anchor and non-anchor alike, the geometric mean of the average relativebinding (ARB) of all peptides carrying j is calculated relative to theremainder of the group, and used as the estimate of j_(t). For Class IIpeptides, if multiple alignments are possible, only the highest scoringalignment is utilized, following an iterative procedure. To calculate analgorithm score of a given peptide in a test set, the ARB valuescorresponding to the sequence of the peptide are multiplied. If thisproduct exceeds a chosen threshold, the peptide is predicted to bind.Appropriate thresholds are chosen as a function of the degree ofstringency of prediction desired.

[0525] Selection of HLA-A2 Supertype Cross-Reactive Peptides

[0526] Protein sequences from 213P1F11 are scanned utilizing motifidentification software, to identify 8-, 9-10- and 11-mer sequencescontaining the HLA-A2-supermotif main anchor specificity. Typically,these sequences are then scored using the protocol described above andthe peptides corresponding to the positive-scoring sequences aresynthesized and tested for their capacity to bind purified HLA-A*0201molecules in vitro (HLA-A*0201 is considered a prototype A2 supertypemolecule).

[0527] These peptides are then tested for the capacity to bind toadditional A2-supertype molecules (A*0202, A*0203, A*0206, and A*6802).Peptides that bind to at least three of the five A2-supertype allelestested are typically deemed A2-supertype cross-reactive binders.Preferred peptides bind at an affinity equal to or less than 500 nM tothree or more HLA-A2 supertype molecules.

[0528] Selection of HLA-A3 Supermotif-Bearing Epitopes

[0529] The 213P1F11 protein sequence(s) scanned above is also examinedfor the presence of peptides with the HLA-A3-supermotif primary anchors.Peptides corresponding to the HLA A3 supermotif-bearing sequences arethen synthesized and tested for binding to HLA-A*0301 and HLA-A* 1101molecules, the molecules encoded by the two most prevalent A3-supertypealleles. The peptides that bind at least one of the two alleles withbinding affinities of ≦500 nM, often ≦200 nM, are then tested forbinding cross-reactivity to the other common A3-supertype alleles (e.g.,A*3101, A*3301, and A*6801) to identify those that can bind at leastthree of the five HLA-A3-supertype molecules tested.

[0530] Selection of HLA-B7 Supermotif Bearing Epitopes

[0531] The 213P1F11 protein(s) scanned above is also analyzed for thepresence of 8-, 9-10-, or 11-mer peptides with the HLA-B7-supermotif.Corresponding peptides are synthesized and tested for binding toHLA-B*0702, the molecule encoded by the most common B7-supertype allele(i.e., the prototype B7 supertype allele). Peptides binding B*0702 withIC₅₀ of ≦500 nM are identified using standard methods. These peptidesare then tested for binding to other common B7-supertype molecules(e.g., B*3501, B*5101, B*5301, and B*5401). Peptides capable of bindingto three or more of the five B7-supertype alleles tested are therebyidentified.

[0532] Selection of A1 and A24 Motif-Bearing Epitopes

[0533] To further increase population coverage, HLA-A1 and -A24 epitopescan also be incorporated into vaccine compositions. An analysis of the213P1F11 protein can also be performed to identify HLA-A1- andA24-motif-containing sequences.

[0534] High affinity and/or cross-reactive binding epitopes that bearother motif and/or supermotifs are identified using analogousmethodology.

Example 14 Confirmation of Immunogenicity

[0535] Cross-reactive candidate CTL A2-supermotif-bearing peptides thatare identified as described herein are selected to confirm in vitroimmunogenicity. Confirmation is performed using the followingmethodology:

[0536] Target Cell Lines for Cellular Screening:

[0537] The 0.221A2.1 cell line, produced by transferring the HLA-A2.1gene into the HLA-A, -B, -C null mutant human B-lymphoblastoid cell line721.221, is used as the peptide-loaded target to measure activity ofHLA-A2.1-restricted CTL. This cell line is grown in RPMI-1640 mediumsupplemented with antibiotics, sodium pyruvate, nonessential amino acidsand 10% (v/v) heat inactivated FCS. Cells that express an antigen ofinterest, or transfectants comprising the gene encoding the antigen ofinterest, can be used as target cells to confirm the ability ofpeptide-specific CTLs to recognize endogenous antigen.

[0538] Primary CTL Induction Cultures:

[0539] Generation of Dendritic Cells (DC): PBMCs are thawed in RPMI with30 μg/ml DNAse, washed twice and resuspended in complete medium(RPMI-1640 plus 5% AB human serum, non-essential amino acids, sodiumpyruvate, L-glutamine and penicillin/streptomycin). The monocytes arepurified by plating 10×10⁶ PBMC/well in a 6-well plate. After 2 hours at37° C., the non-adherent cells are removed by gently shaking the platesand aspirating the supernatants. The wells are washed a total of threetimes with 3 ml RPMI to remove most of the non-adherent and looselyadherent cells. Three ml of complete medium containing 50 ng/ml ofGM-CSF and 1,000 U/ml of IL-4 are then added to each well. TNFα is addedto the DCs on day 6 at 75 ng/1 ml and the cells are used for CTLinduction cultures on day 7.

[0540] Induction of CTL with DC and Peptide: CD8+ T-cells are isolatedby positive selection with Dynal immunomagnetic beads (Dynabeads® M-450)and the detacha-bead® reagent. Typically about 200-250×10⁶ PBMC areprocessed to obtain 24×10⁶ CD8⁺ T-cells (enough for a 48-well plateculture). Briefly, the PBMCs are thawed in RPMI with 30 μg/ml DNAse,washed once with PBS containing 1% human AB serum and resuspended inPBS/1% AB serum at a concentration of 20×10⁶cells/ml. The magnetic beadsare washed 3 times with PBS/AB serum, added to the cells (140 μlbeads/20×10⁶ cells) and incubated for 1 hour at 4° C. with continuousmixing. The beads and cells are washed 4×with PBS/AB serum to remove thenonadherent cells and resuspended at 100×10⁶ cells/mil (based on theoriginal cell number) in PBS/AB serum containing 100 μl/ml detacha-bead®reagent and 30 μg/ml DNAse. The mixture is incubated for 1 hour at roomtemperature with continuous mixing. The beads are washed again withPBS/AB/DNAse to collect the CD8+T-cells. The DC are collected andcentrifuged at 1300 rpm for 5-7 minutes, washed once with PBS with 1%BSA, counted and pulsed with 40 μg/ml of peptide at a cell concentrationof 1-2×10⁶/ml in the presence of 3 μg/ml β₂-microglobulin for 4 hours at20° C. The DC are then irradiated (4,200 rads), washed 1 time withmedium and counted again.

[0541] Setting up induction cultures: 0.25 ml cytokine-generated DC (at1×10⁵ cells/ml) are co-cultured with 0.25 ml of CD8+ T-cells (at 2×10⁶cell/ml) in each well of a 48-well plate in the presence of 10 ng/ml ofIL-7. Recombinant human IL-10 is added the next day at a finalconcentration of 10 ng/ml and rhuman IL-2 is added 48 hours later at 10IU/ml.

[0542] Restimulation of the induction cultures with peptide-pulsedadherent cells: Seven and fourteen days after the primary induction, thecells are restimulated with peptide-pulsed adherent cells. The PBMCs arethawed and washed twice with RPMI and DNAse. The cells are resuspendedat 5×10⁶ cells/ml and irradiated at ˜4200 rads. The PBMCs are plated at2×10⁶ in 0.5 ml complete medium per well and incubated for 2 hours at37° C. The plates are washed twice with RPMI by tapping the plate gentlyto remove the nonadherent cells and the adherent cells pulsed with 10μg/ml of peptide in the presence of 3 μg/ml B2 microglobulin in 0.25 mlRPMI/5%AB per well for 2 hours at 37° C. Peptide solution from each wellis aspirated and the wells are washed once with RPMI. Most of the mediais aspirated from the induction cultures (CD8+ cells) and brought to 0.5ml with fresh media. The cells are then transferred to the wellscontaining the peptide-pulsed adherent cells. Twenty four hours laterrecombinant human IL-10 is added at a final concentration of 10 ng/mland recombinant human IL2 is added the next day and again 2-3 days laterat 501U/ml (Tsai et al., Critical Reviews in Immunology 18(1-2):65-75,1998). Seven days later, the cultures are assayed for CTL activity in a⁵¹Cr release assay. In some experiments the cultures are assayed forpeptide-specific recognition in the in situ IFNγ ELISA at the time ofthe second restimulation followed by assay of endogenous recognition 7days later. After expansion, activity is measured in both assays for aside-by-side comparison.

[0543] Measurement of CTL Lytic Activity by ⁵¹Cr Release.

[0544] Seven days after the second restimulation, cytotoxicity isdetermined in a standard (5 hr) ⁵¹Cr release assay by assayingindividual wells at a single E:T. Peptide-pulsed targets are prepared byincubating the cells with 10 μg/ml peptide overnight at 37° C.

[0545] Adherent target cells are removed from culture flasks withtrypsin-EDTA. Target cells are labeled with 200 μCi of ⁵¹Cr sodiumchromate (Dupont, Wilmington, Del.) for 1 hour at 37° C. Labeled targetcells are resuspended at 10⁶ per ml and diluted 1:10 with K562 cells ata concentration of 3.3×10⁶/ml (an NK-sensitive erythroblastoma cell lineused to reduce non-specific lysis). Target cells (100 μl) and effectors(100 μl) are plated in 96 well round-bottom plates and incubated for 5hours at 37° C. At that time, 100 μl of supernatant are collected fromeach well and percent lysis is determined according to the formula:

[(cpm of the test sample−cpm of the spontaneous ⁵¹Cr releasesample)/(cpm of the maximal ⁵¹Cr release sample−cpm of the spontaneous⁵¹Cr release sample)]×100.

[0546] Maximum and spontaneous release are determined by incubating thelabeled targets with 1% Triton X-100 and media alone, respectively. Apositive culture is defined as one in which the specific lysis(sample-background) is 10% or higher in the case of individual wells andis 15% or more at the two highest E:T ratios when expanded cultures areassayed.

[0547] In Situ Measurement of Human IFNγ Production as an Indicator ofPeptide-Specific and Endogenous Recognition

[0548] Immulon 2 plates are coated with mouse anti-human IFNγ monoclonalantibody (4 μg/ml 0.1 M NaHCO₃, pH 8.2) overnight at 4° C. The platesare washed with Ca²⁺, Mg²⁺-free PBS/0.05% Tween 20 and blocked withPBS/10% FCS for two hours, after which the CTLs (100 μl/well) andtargets (100 μl/well) are added to each well, leaving empty wells forthe standards and blanks (which received media only). The target cells,either peptide-pulsed or endogenous targets, are used at a concentrationof 1×10⁶ cells/ml. The plates are incubated for 48 hours at 37° C. with5% CO₂.

[0549] Recombinant human IFN-ganma is added to the standard wellsstarting at 400 pg or 1200 pg/100 microliter/well and the plateincubated for two hours at 37° C. The plates are washed and 100 μl ofbiotinylated mouse anti-human IFN-gamma monoclonal antibody (2microgram/ml in PBS/3%FCS/0.05% Tween 20) are added and incubated for 2hours at room temperature. After washing again, 100 microliterHRP-streptavidin (1:4000) are added and the plates incubated for onehour at room temperature. The plates are then washed 6× with washbuffer, 100 microliter/well developing solution (TMB 1:1) are added, andthe plates allowed to develop for 5-15 minutes. The reaction is stoppedwith 50 microliter/well 1M H₃PO₄ and read at OD450. A culture isconsidered positive if it measured at least 50 pg of IFN-gamma/wellabove background and is twice the background level of expression.

[0550] CTL Expansion.

[0551] Those cultures that demonstrate specific lytic activity againstpeptide-pulsed targets and/or tumor targets are expanded over a two weekperiod with anti-CD3. Briefly, 5×10⁴ CD8+ cells are added to a T25 flaskcontaining the following: 1×10⁶ irradiated (4,200 rad) PBMC (autologousor allogeneic) per ml, 2×10⁵ irradiated (8,000 rad) EBV—transformedcells per ml, and OKT3 (anti-CD3) at 30 ng per ml in RPMI-1640containing 10% (v/v) human AB serum, non-essential amino acids, sodiumpyruvate, 25 μM 2-mercaptoethanol, L-glutamine andpenicillin/streptomycin. Recombinant human IL2 is added 24 hours laterat a final concentration of 200 IU/ml and every three days thereafterwith fresh media at 50 IU/ml. The cells are split if the cellconcentration exceeds 1×10⁶/ml and the cultures are assayed between days13 and 15 at E:T ratios of 30, 10, 3 and 1:1 in the ⁵¹Cr release assayor at 1×10⁶/ml in the in situ IFNγ assay using the same targets asbefore the expansion.

[0552] Cultures are expanded in the absence of anti-CD3⁺ as follows.Those cultures that demonstrate specific lytic activity against peptideand endogenous targets are selected and 5×10⁴ CD8⁺ cells are added to aT25 flask containing the following: 1×10⁶ autologous PBMC per ml whichhave been peptide-pulsed with 10 μg/ml peptide for two hours at 37° C.and irradiated (4,200 rad); 2×10⁵ irradiated (8,000 rad) EBV-transformedcells per ml RPMI-1640 containing 10%(v/v) human AB serum, non-essentialAA, sodium pyruvate, 25 mM 2-ME, L-glutamine and gentamicin.

[0553] Immunogenicity of A2 Supermotif-Bearing Peptides

[0554] A2-supermotif cross-reactive binding peptides are tested in thecellular assay for the ability to induce peptide-specific CTL in normalindividuals. In this analysis, a peptide is typically considered to bean epitope if it induces peptide-specific CTLs in at least individuals,and preferably, also recognizes the endogenously expressed peptide.

[0555] Immunogenicity can also be confirmed using PBMCs isolated frompatients bearing a tumor that expresses 213P11. Briefly, PBMCs areisolated from patients, re-stimulated with peptide-pulsed monocytes andassayed for the ability to recognize peptide-pulsed target cells as wellas transfected cells endogenously expressing the antigen.

[0556] Evaluation of A*03/A11 Immunogenicity

[0557] HLA-A3 supermotif-bearing cross-reactive binding peptides arealso evaluated for immunogenicity using methodology analogous for thatused to evaluate the immunogenicity of the HLA-A2 supermotif peptides.

[0558] Evaluation of B7 Immunogenicity

[0559] Immunogenicity screening of the B7-supertype cross-reactivebinding peptides identified as set forth herein are confirmed in amanner analogous to the confirmation of A2-and A3-supermotif-bearingpeptides.

[0560] Peptides bearing other supermotifs/motifs, e.g., HLA-A 1, HLA-A24etc. are also confirmed using similar methodology

Example 15 Implementation of the Extended Supermotif to Improve theBinding Capacity of Native Epitopes by Creating Analogs

[0561] HLA motifs and supermotifs (comprising primary and/or secondaryresidues) are useful in the identification and preparation of highlycross-reactive native peptides, as demonstrated herein. Moreover, thedefinition of HLA motifs and supermotifs also allows one to engineerhighly cross-reactive epitopes by identifying residues within a nativepeptide sequence which can be analoged to confer upon the peptidecertain characteristics, e.g. greater cross-reactivity within the groupof HLA molecules that comprise a supertype, and/or greater bindingaffinity for some or all of those HLA molecules. Examples of analogingpeptides to exhibit modulated binding affinity are set forth in thisexample.

[0562] Analoging at Primary Anchor Residues

[0563] Peptide engineering strategies are implemented to furtherincrease the cross-reactivity of the epitopes. For example, the mainanchors of A2-supermotif-bearing peptides are altered, for example, tointroduce a preferred L, I, V, or M at position 2, and I or V at theC-terminus.

[0564] To analyze the cross-reactivity of the analog peptides, eachengineered analog is initially tested for binding to the prototype A2supertype allele A*0201, then, if A*0201 binding capacity is maintained,for A2-supertype cross-reactivity.

[0565] Alternatively, a peptide is confirmed as binding one or allsupertype members and then analoged to modulate binding affinity to anyone (or more) of the supertype members to add population coverage.

[0566] The selection of analogs for inmmunogenicity in a cellularscreening analysis is typically further restricted by the capacity ofthe parent wild type (WT) peptide to bind at least weakly, i.e., bind atan IC₅₀ of 5000 nM or less, to three of more A2 supertype alleles. Therationale for this requirement is that the WT peptides must be presentendogenously in sufficient quantity to be biologically relevant.Analoged peptides have been shown to have increased immunogenicity andcross-reactivity by T cells specific for the parent epitope (see, e.g.,Parkhurst et al, J. Immunol. 157:2539, 1996; and Pogue et al., Proc.Natl. Acad. Sci. USA 92:8166, 1995).

[0567] In the cellular screening of these peptide analogs, it isimportant to confirm that analog-specific CTLs are also able torecognize the wild-type peptide and, when possible, target cells thatendogenously express the epitope.

[0568] Analoging of HLA-A3 and B7-Supermotif-Bearing Peptides

[0569] Analogs of HLA-A3 supermotif-bearing epitopes are generated usingstrategies similar to those employed in analoging HLA-A2supermotif-bearing peptides. For example, peptides binding to 3/5 of theA3-supertype molecules are engineered at primary anchor residues topossess a preferred residue (V, S, M, or A) at position 2.

[0570] The analog peptides are then tested for the ability to bind A*03and A*11 (prototype A3 supertype alleles). Those peptides thatdemonstrate <500 nM binding capacity are then confirmed as havingA3-supertype cross-reactivity.

[0571] Similarly to the A2- and A3-motif bearing peptides, peptidesbinding 3 or more B7-supertype alleles can be improved, where possible,to achieve increased cross-reactive binding or greater binding affinityor binding half life. B7 supermotif-bearing peptides are, for example,engineered to possess a preferred residue (V, I, L, or F) at theC-terminal primary anchor position, as demonstrated by Sidney et al. (J.Immunol. 157:3480-3490, 1996).

[0572] Analoging at primary anchor residues of other motif and/orsupermotif-bearing epitopes is performed in a like manner.

[0573] The analog peptides are then be confirmed for immunogenicity,typically in a cellular screening assay. Again, it is generallyimportant to demonstrate that analog-specific CTLs are also able torecognize the wild-type peptide and, when possible, targets thatendogenously express the epitope.

[0574] Analoging at Secondary Anchor Residues

[0575] Moreover, HLA supermotifs are of value in engineering highlycross-reactive peptides and/or peptides that bind HLA molecules withincreased affinity by identifying particular residues at secondaryanchor positions that are associated with such properties. For example,the binding capacity of a B7 supermotif-bearing peptide with an Fresidue at position 1 is analyzed. The peptide is then analoged to, forexample, substitute L for F at position 1. The analoged peptide isevaluated for increased binding affinity, binding half life and/orincreased cross-reactivity. Such a procedure identifies analogedpeptides with enhanced properties.

[0576] Engineered analogs with sufficiently improved binding capacity orcross-reactivity can also be tested for immunogenicity inHLA-B7-transgenic mice, following for example, IFA immunization orlipopeptide immunization. Analoged peptides are additionally tested forthe ability to stimulate a recall response using PBMC from patients with213P1F11-expressing tumors.

[0577] Other Analoging Strategies

[0578] Another form of peptide analoging, unrelated to anchor positions,involves the substitution of a cysteine with α-amino butyric acid. Dueto its chemical nature, cysteine has the propensity to form disulfidebridges and sufficiently alter the peptide structurally so as to reducebinding capacity. Substitution of α-amino butyric acid for cysteine notonly alleviates this problem, but has been shown to improve binding andcrossbinding capabilities in some instances (see, e.g., the review bySette et al., In: Persistent Viral Infections, Eds. R. Ahlned and I.Chen, John Wiley & Sons, England, 1999).

[0579] Thus, by the use of single amino acid substitutions, the bindingproperties and/or cross-reactivity of peptide ligands for HLA supertypemolecules can be modulated.

Example 16 Identification and Confirmation of 213P1F11-Derived Sequenceswith HLA-DR Binding Motifs

[0580] Peptide epitopes bearing an HLA class II supermotif or motif areidentified and confirmed as outlined below using methodology similar tothat described for HLA Class I peptides.

[0581] Selection of HLA-DR-Supermotif-Bearing Epitopes.

[0582] To identify 213P1F11-derived, HLA class II HTL epitopes, a213P1F11 antigen is analyzed for the presence of sequences bearing anHLA-DR-motif or supermotif. Specifically, 15-mer sequences are selectedcomprising a DR-supermotif, comprising a 9-mer core, and three-residueN- and C-terminal flanking regions (15 amino acids total).

[0583] Protocols for predicting peptide binding to DR molecules havebeen developed (Southwood et al., J. Immunol. 160:3363-3373, 1998).These protocols, specific for individual DR molecules, allow thescoring, and ranking, of 9-mer core regions. Each protocol not onlyscores peptide sequences for the presence of DR-supermotif primaryanchors (i.e., at position 1 and position 6) within a 9-mer core, butadditionally evaluates sequences for the presence of secondary anchors.Using allele-specific selection tables (see, e.g., Southwood et al.,ibid.), it has been found that these protocols efficiently selectpeptide sequences with a high probability of binding a particular DRmolecule. Additionally, it has been found that performing theseprotocols in tandem, specifically those for DR1, DR4w4, and DR7, canefficiently select DR cross-reactive peptides.

[0584] The 213P1F11-derived peptides identified above are tested fortheir binding capacity for various common HLA-DR molecules. All peptidesare initially tested for binding to the DR molecules in the primarypanel: DR1, DR4w4, and DR7. Peptides binding at least two of these threeDR molecules are then tested for binding to DR2w2 β1, DR2w2 β2, DR6w19,and DR9 molecules in secondary assays. Finally, peptides binding atleast two of the four secondary panel DR molecules, and thuscumulatively at least four of seven different DR molecules, are screenedfor binding to DR4w15, DR5w11, and DR8w2 molecules in tertiary assays.Peptides binding at least seven of the ten DR molecules comprising theprimary, secondary, and tertiary screening assays are consideredcross-reactive DR binders. 213P1F11-derived peptides found to bindcommon HLA-DR alleles are of particular interest.

[0585] Selection of DR3 Motif Peptides

[0586] Because HLA-DR3 is an allele that is prevalent in Caucasian,Black, and Hispanic populations, DR3 binding capacity is a relevantcriterion in the selection of HTL epitopes. Thus, peptides shown to becandidates may also be assayed for their DR3 binding capacity. However,in view of the binding specificity of the DR3 motif, peptides bindingonly to DR3 can also be considered as candidates for inclusion in avaccine formulation.

[0587] To efficiently identify peptides that bind DR3, target 213P1F11antigens are analyzed for sequences carrying one of the two DR3-specificbinding motifs reported by Geluk et al. (J. Immunol. 152:5742-5748,1994). The corresponding peptides are then synthesized and confirmed ashaving the ability to bind DR3 with an affinity of 1 μM or better, i.e.,less than 1 μM. Peptides are found that meet this binding criterion andqualify as HLA class II high affinity binders.

[0588] DR3 binding epitopes identified in this manner are included invaccine compositions with DR supermotif-bearing peptide epitopes.

[0589] Similarly to the case of HLA class I motif-bearing peptides, theclass II motif-bearing peptides are analoged to improve affinity orcross-reactivity. For example, aspartic acid at position 4 of the 9-mercore sequence is an optimal residue for DR3 binding, and substitutionfor that residue often improves DR 3 binding.

Example 17 Immunogenicity of 213P1F11-Derived HTL Epitopes

[0590] This example determines immunogenic DR supermotif- and DR3motif-bearing epitopes among those identified using the methodology setforth herein.

[0591] Immunogenicity of HTL epitopes are confirmed in a manneranalogous to the determination of immunogenicity of CTL epitopes, byassessing the ability to stimulate HTL responses and/or by usingappropriate transgenic mouse models. Immunogenicity is determined byscreening for: 1.) in vitro primary induction using normal PBMC or 2.)recall responses from patients who have 213P1F11-expressing tumors.

Example 18 Calculation of Phenotypic Frequencies of HLA-Supertypes inVarious Ethnic Backgrounds to Determine Breadth of Population Coverage

[0592] This example illustrates the assessment of the breadth ofpopulation coverage of a vaccine composition comprised of multipleepitopes comprising multiple supermotifs and/or motifs.

[0593] In order to analyze population coverage, gene frequencies of HLAalleles are determined. Gene frequencies for each HLA allele arecalculated from antigen or allele frequencies utilizing the binomialdistribution formulae gf=1−(SQRT(1−af)) (see, e.g., Sidney et al., HumanImmunol. 45:79-93, 1996). To obtain overall phenotypic frequencies,cumulative gene frequencies are calculated, and the cumulative antigenfrequencies derived by the use of the inverse formula [af=1−(1−Cgf)²].

[0594] Where frequency data is not available at the level of DNA typing,correspondence to the serologically defined antigen frequencies isassumed. To obtain total potential supertype population coverage nolinkage disequilibrium is assumed, and only alleles confirmed to belongto each of the supertypes are included (minimal estimates). Estimates oftotal potential coverage achieved by inter-loci combinations are made byadding to the A coverage the proportion of the non-A covered populationthat could be expected to be covered by the B alleles considered (e.g.,total=A+B*(1−A)). Confirmed members of the A3-like supertype are A3,A11, A31, A*3301, and A*6801. Although the A3-like supertype may alsoinclude A34, A66, and A*7401, these alleles were not included in overallfrequency calculations. Likewise, confirmed members of the A2-likesupertype family are A*0201, A*0202, A*0203, A*0204, A*0205, A*0206,A*0207, A*6802, and A*6901. Finally, the B7-like supertype-confirmedalleles are: B7, B*3501-03, B51, B*5301, B*5401, B*5501-2, B*5601,B*6701, and B*7801 (potentially also B*1401, B*3504-06, B*4201, andB*5602).

[0595] Population coverage achieved by combining the A2-, A3- andB7-supertypes is approximately 86% in five major ethnic groups. Coveragemay be extended by including peptides bearing the A1 and A24 motifs. Onaverage, A1 is present in 12% and A24 in 29% of the population acrossfive different major ethnic groups (Caucasian, North American Black,Chinese, Japanese, and Hispanic). Together, these alleles arerepresented with an average frequency of 39% in these same ethnicpopulations. The total coverage across the major ethnicities when A1 andA24 are combined with the coverage of the A2-, A3- and B7-supertypealleles is >95%. An analogous approach can be used to estimatepopulation coverage achieved with combinations of class II motif-bearingepitopes.

[0596] Immunogenicity studies in humans (e.g., Bertoni et al., J. Clin.Invest. 100:503, 1997; Doolan et al., Immunity 7:97, 1997; and Threlkeldet al., J. Immunol 159:1648, 1997) have shown that highly cross-reactivebinding peptides are almost always recognized as epitopes. The use ofhighly cross-reactive binding peptides is an important selectioncriterion in identifying candidate epitopes for inclusion in a vaccinethat is immunogenic in a diverse population.

[0597] With a sufficient number of epitopes (as disclosed herein andfrom the art), an average population coverage is predicted to be greaterthan 95% in each of five major ethnic populations. The game theory MonteCarlo simulation analysis, which is known in the art (see e.g., Osborne,M. J. and Rubinstein, A. “A course in game theory” MIT Press, 1994), canbe used to estimate what percentage of the individuals in a populationcomprised of the Caucasian, North American Black, Japanese, Chinese, andHispanic ethnic groups would recognize the vaccine epitopes describedherein. A preferred percentage is 90%. A more preferred percentage is95%.

Example 19 CTL Recognition of Endogenously Processed Antigens AfterPriming

[0598] This example confirms that CTL induced by native or analogedpeptide epitopes identified and selected as described herein recognizeendogenously synthesized, i.e., native antigens.

[0599] Effector cells isolated from transgenic mice that are immunizedwith peptide epitopes, for example HLA-A2 supermotif-bearing epitopes,are re-stimulated in vitro using peptide-coated stimulator cells. Sixdays later, effector cells are assayed for cytotoxicity and the celllines that contain peptide-specific cytotoxic activity are furtherre-stimulated. An additional six days later, these cell lines are testedfor cytotoxic activity on ⁵¹Cr labeled Jurkat-A2.1/K^(b) target cells inthe absence or presence of peptide, and also tested on ⁵¹Cr labeledtarget cells bearing the endogenously synthesized antigen, i.e. cellsthat are stably transfected with 213P1F11 expression vectors.

[0600] The results demonstrate that CTL lines obtained from animalsprimed with peptide epitope recognize endogenously synthesized 213P1F11antigen. The choice of transgenic mouse model to be used for such ananalysis depends upon the epitope(s) that are being evaluated. Inaddition to HLA-A*0201/K^(b) transgenic mice, several other transgenicmouse models including mice with human A11, which may also be used toevaluate A3 epitopes, and B7 alleles have been characterized and others(e.g., transgenic mice for HLA-A 1 and A24) are being developed. HLA-DR1and HLA-DR3 mouse models have also been developed, which may be used toevaluate HTL epitopes.

Example 20 Activity of CTL-HTL Conjugated Epitopes in Transgenic Mice

[0601] This example illustrates the induction of CTLs and HTLs intransgenic mice, by use of a 213P1F11-derived CTL and HTL peptidevaccine compositions. The vaccine composition used herein comprisepeptides to be administered to a patient with a 213P1F11-expressingtumor. The peptide composition can comprise multiple CTL and/or HTLepitopes. The epitopes are identified using methodology as describedherein. This example also illustrates that enhanced immunogenicity canbe achieved by inclusion of one or more HTL epitopes in a CTL vaccinecomposition; such a peptide composition can comprise an HTL epitopeconjugated to a CTL epitope. The CTL epitope can be one that binds tomultiple HLA family members at an affinity of 500 nM or less, or analogsof that epitope. The peptides may be lipidated, if desired.

[0602] Immunization procedures: Immunization of transgenic mice isperformed as described (Alexander et al., J. Immunol. 159:4753-4761,1997). For example, A2/Kb mice, which are transgenic for the human HLAA2.1 allele and are used to confirm the immunogenicity of HLA-A*0201motif- or HLA-A2 supermotif-bearing epitopes, and are primedsubcutaneously (base of the tail) with a 0.1 ml of peptide in IncompleteFreund's Adjuvant, or if the peptide composition is a lipidated CTL/HTLconjugate, in DMSO/saline, or if the peptide composition is apolypeptide, in PBS or Incomplete Freund's Adjuvant. Seven days afterpriming, splenocytes obtained from these animals are restimulated withsyngenic irradiated LPS-activated lymphoblasts coated with peptide.

[0603] Cell lines: Target cells for peptide-specific cytotoxicity assaysare Jurkat cells transfected with the HLA-A2.1/Kb chimeric gene (e.g.,Vitiello et al., J. Exp. Med. 173:1007, 1991) In vitro CTL activation.One week after priming, spleen cells (30×10⁶ cells/flask) areco-cultured at 37° C. with syngeneic, irradiated (3000 rads), peptidecoated lymphoblasts (10×10⁶ cells/flask) in 10 ml of culture medium/T25flask. After six days, effector cells are harvested and assayed forcytotoxic activity.

[0604] Assay for cytotoxic activity: Target cells (1.0 to 1.5×10⁶) areincubated at 37° C. in the presence of 200 μl of ⁵¹Cr. After 60 minutes,cells are washed three times and resuspended in R10 medium. Peptide isadded where required at a concentration of 1 μg/ml. For the assay, 10⁴⁵¹Cr-labeled target cells are added to different concentrations ofeffector cells (final volume of 200 μl) in U-bottom 96-well plates.After a six hour incubation period at 37° C., a 0.1 ml aliquot ofsupernatant is removed from each well and radioactivity is determined ina Micromedic automatic gamma counter. The percent specific lysis isdetermined by the formula: percent specific release=100×(experimentalrelease−spontaneous release)/(maximum release−spontaneous release). Tofacilitate comparison between separate CTL assays run under the sameconditions, % ⁵¹Cr release data is expressed as lytic units/10⁶ cells.One lytic unit is arbitrarily defined as the number of effector cellsrequired to achieve 30% lysis of 10,000 target cells in a six hour ⁵¹Crrelease assay. To obtain specific lytic units/10⁶, the lytic units/10⁶obtained in the absence of peptide is subtracted from the lyticunits/10⁶ obtained in the presence of peptide. For example, if 30% ⁵¹Crrelease is obtained at the effector (E): target (T) ratio of 50:1 (i.e.,5×10⁵ effector cells for 10,000 targets) in the absence of peptide and5:1 (i.e., 5×10⁴ effector cells for 10,000 targets) in the presence ofpeptide, the specific lytic units would be:[(1/50,000)−(1/500,000)]×10⁶=18 LU.

[0605] The results are analyzed to assess the magnitude of the CTLresponses of animals injected with the immunogenic CTL/HTL conjugatevaccine preparation and are compared to the magnitude of the CTLresponse achieved using, for example, CTL epitopes as outlined above inthe Example entitled “Confirmation of Immunogenicity.” Analyses similarto this may be performed to confirm the immunogenicity of peptideconjugates containing multiple CTL epitopes and/or multiple HTLepitopes. In accordance with these procedures, it is found that a CTLresponse is induced, and concomitantly that an HTL response is inducedupon administration of such compositions.

Example 21 Selection of CTL and HTL Epitopes for Inclusion in a213P1F11-Specific Vaccine

[0606] This example illustrates a procedure for selecting peptideepitopes for vaccine compositions of the invention. The peptides in thecomposition can be in the form of a nucleic acid sequence, either singleor one or more sequences (i.e., minigene) that encodes peptide(s), orcan be single and/or polyepitopic peptides.

[0607] The following principles are utilized when selecting a pluralityof epitopes for inclusion in a vaccine composition. Each of thefollowing principles is balanced in order to make the selection.

[0608] Epitopes are selected which, upon administration, mimic immuneresponses that are correlated with 213P1F11 clearance. The number ofepitopes used depends on observations of patients who spontaneouslyclear 213P1F11. For example, if it has been observed that patients whospontaneously clear 213P1F11-expressing cells generate an immuneresponse to at least three (3) from 213P F11 antigen, then at leastthree epitopes should be included for HLA class I. A similar rationaleis used to determine HLA class II epitopes.

[0609] Epitopes are often selected that have a binding affinity of anIC₅₀ of 500 nM or less for an HLA class I molecule, or for class II, anIC₅₀ of 1000 nM or less; or HLA Class I peptides with high bindingscores from the BIMAS web site, at URL bimas.dcrt.nih.gov/.

[0610] In order to achieve broad coverage of the vaccine through out adiverse population, sufficient supermotif bearing peptides, or asufficient array of allele-specific motif bearing peptides, are selectedto give broad population coverage. In one embodiment, epitopes areselected to provide at least 80% population coverage. A Monte Carloanalysis, a statistical evaluation known in the art, can be employed toassess breadth, or redundancy, of population coverage.

[0611] When creating polyepitopic compositions, or a minigene thatencodes same, it is typically desirable to generate the smallest peptidepossible that encompasses the epitopes of interest. The principlesemployed are similar, if not the same, as those employed when selectinga peptide comprising nested epitopes. For example, a protein sequencefor the vaccine composition is selected because it has maximal number ofepitopes contained within the sequence, i.e., it has a highconcentration of epitopes. Epitopes may be nested or overlapping (i.e.,frame shifted relative to one another). For example, with overlappingepitopes, two 9-mer epitopes and one 10-mer epitope can be present in a10 amino acid peptide. Each epitope can be exposed and bound by an HLAmolecule upon administration of such a peptide. A multi-epitopic,peptide can be generated synthetically, recombinantly, or via cleavagefrom the native source. Alternatively, an analog can be made of thisnative sequence, whereby one or more of the epitopes comprisesubstitutions that alter the cross-reactivity and/or binding affinityproperties of the polyepitopic peptide. Such a vaccine composition isadministered for therapeutic or prophylactic purposes. This embodimentprovides for the possibility that an as yet undiscovered aspect ofimmune system processing will apply to the native nested sequence andthereby facilitate the production of therapeutic or prophylactic immuneresponse-inducing vaccine compositions. Additionally such an embodimentprovides for the possibility of motif-bearing epitopes for an HLA makeupthat is presently unknown. Furthermore, this embodiment (absent thecreating of any analogs) directs the immune response to multiple peptidesequences that are actually present in 213P1F11, thus avoiding the needto evaluate any junctional epitopes. Lastly, the embodiment provides aneconomy of scale when producing nucleic acid vaccine compositions.Related to this embodiment, computer programs can be derived inaccordance with principles in the art, which identify in a targetsequence, the greatest number of epitopes per sequence length.

[0612] A vaccine composition comprised of selected peptides, whenadministered, is safe, efficacious, and elicits an immune responsesimilar in magnitude to an immune response that controls or clears cellsthat bear or overexpress 213P1F11.

Example 22 Construction of “Minigene” Multi-Epitope DNA Plasmids

[0613] This example discusses the construction of a minigene expressionplasmid. Minigene plasmids may, of course, contain variousconfigurations of B cell, CTL and/or HTL epitopes or epitope analogs asdescribed herein.

[0614] A minigene expression plasmid typically includes multiple CTL andHTL peptide epitopes. In the present example, HLA-A2, -A3, -B7supermotif-bearing peptide epitopes and HLA-A1 and -A24 motif-bearingpeptide epitopes are used in conjunction with DR supermotif-bearingepitopes and/or DR3 epitopes. HLA class I supermotif or motif-bearingpeptide epitopes derived 213P1F11, are selected such that multiplesupermotifs/motifs are represented to ensure broad population coverage.Similarly, HLA class II epitopes are selected from 213P1F11 to providebroad population coverage, i.e. both HLA DR-1-4-7 supermotif-bearingepitopes and HLA DR-3 motif-bearing epitopes are selected for inclusionin the minigene construct. The selected CTL and HTL epitopes are thenincorporated into a minigene for expression in an expression vector.

[0615] Such a construct may additionally include sequences that directthe HTL epitopes to the endoplasmic reticulum. For example, the Iiprotein may be fused to one or more HTL epitopes as described in theart, wherein the CLIP sequence of the Ii protein is removed and replacedwith an HLA class II epitope sequence so that HLA class II epitope isdirected to the endoplasmic reticulum, where the epitope binds to an HLAclass II molecules.

[0616] This example illustrates the methods to be used for constructionof a minigene-bearing expression plasmid. Other expression vectors thatmay be used for minigene compositions are available and known to thoseof skill in the art.

[0617] The minigene DNA plasmid of this example contains a consensusKozak sequence and a consensus murine kappa Ig-light chain signalsequence followed by CTL and/or HTL epitopes selected in accordance withprinciples disclosed herein. The sequence encodes an open reading framefused to the Myc and His antibody epitope tag coded for by the pcDNA 3.1Myc-His vector.

[0618] Overlapping oligonucleotides that can, for example, average about70 nucleotides in length with 15 nucleotide overlaps, are synthesizedand HPLC-purified. The oligonucleotides encode the selected peptideepitopes as well as appropriate linker nucleotides, Kozak sequence, andsignal sequence. The final multiepitope minigene is assembled byextending the overlapping oligonucleotides in three sets of reactionsusing PCR. A Perkin/Elmer 9600 PCR machine is used and a total of 30cycles are performed using the following conditions: 95° C. for 15 sec,annealing temperature (5° below the lowest calculated Tm of each primerpair) for 30 sec, and 72° C. for 1 min.

[0619] For example, a minigene is prepared as follows. For a first PCRreaction, 5 μg of each of two oligonucleotides are annealed andextended: In an example using eight oligonucleotides, i.e., four pairsof primers, oligonucleotides 1+2, 3+4, 5+6, and 7+8 are combined in 100μl reactions containing Pfu polymerase buffer (1×=10 mM KCL, 10 mM(NH4)₂SO₄, 20 mM Tris-chloride, pH 8.75, 2 mM MgSO₄, 0.1% Triton X-100,100 μg/ml BSA), 0.25 mM each dNTP, and 2.5 U of Pfu polymerase. Thefull-length dimer products are gel-purified, and two reactionscontaining the product of 1+2 and 3+4, and the product of 5+6 and 7+8are mixed, annealed, and extended for 10 cycles. Half of the tworeactions are then mixed, and 5 cycles of annealing and extensioncarried out before flanking primers are added to amplify the full lengthproduct. The full-length product is gel-purified and cloned intopCR-blunt (Invitrogen) and individual clones are screened by sequencing.

Example 23 The Plasmid Construct and the Degree to Which it InducesImmunogenicity

[0620] The degree to which a plasmid construct, for example a plasmidconstructed in accordance with the previous Example, is able to induceimmunogenicity is confirmed in vitro by determining epitope presentationby APC following transduction or transfection of the APC with anepitope-expressing nucleic acid construct. Such a study determines“antigenicity” and allows the use of human APC. The assay determines theability of the epitope to be presented by the APC in a context that isrecognized by a T cell by quantifying the density of epitope-HLA class Icomplexes on the cell surface. Quantitation can be performed by directlymeasuring the amount of peptide eluted from the APC (see, e.g., Sijts etal., J. Immunol. 156:683-692, 1996; Demotz et al., Nature 342:682-684,1989); or the number of peptide-HLA class I complexes can be estimatedby measuring the amount of lysis or lymphokine release induced bydiseased or transfected target cells, and then determining theconcentration of peptide necessary to obtain equivalent levels of lysisor lymphokine release (see, e.g., Kageyama et al., J. Immunol.154:567-576, 1995).

[0621] Alternatively, immunogenicity is confirmed through in vivoinjections into mice and subsequent in vitro assessment of CTL and HTLactivity, which are analyzed using cytotoxicity and proliferationassays, respectively, as detailed e.g., in Alexander et al., Immunity1:751-761, 1994.

[0622] For example, to confirm the capacity of a DNA minigene constructcontaining at least one HLA-A2 supermotif peptide to induce CTLs invivo, HLA-A2.11 K^(b) transgenic mice, for example, are immunizedintramuscularly with 100 μg of naked cDNA. As a means of comparing thelevel of CTLs induced by cDNA immunization, a control group of animalsis also immunized with an actual peptide composition that comprisesmultiple epitopes synthesized as a single polypeptide as they would beencoded by the minigene.

[0623] Splenocytes from immunized animals are stimulated twice with eachof the respective compositions (peptide epitopes encoded in the minigeneor the polyepitopic peptide), then assayed for peptide-specificcytotoxic activity in a ⁵¹Cr release assay. The results indicate themagnitude of the CTL response directed against the A2-restrictedepitope, thus indicating the in vivo immunogenicity of the minigenevaccine and polyepitopic vaccine.

[0624] It is, therefore, found that the minigene elicits immuneresponses directed toward the HLA-A2 supermotif peptide epitopes as doesthe polyepitopic peptide vaccine. A similar analysis is also performedusing other HLA-A3 and HLA-B7 transgenic mouse models to assess CTLinduction by HLA-A3 and HLA-B7 motif or supermotif epitopes, whereby itis also found that the minigene elicits appropriate immune responsesdirected toward the provided epitopes.

[0625] To confirm the capacity of a class II epitope-encoding minigeneto induce HTLs in vivo, DR transgenic mice, or for those epitopes thatcross react with the appropriate mouse MHC molecule, I-A^(b)-restrictedmice, for example, are immunized intramuscularly with 100 μg of plasmidDNA. As a means of comparing the level of HTLs induced by DNAimmunization, a group of control animals is also immunized with anactual peptide composition emulsified in complete Freund's adjuvant.CD4+ T cells, i.e. HTLs, are purified from splenocytes of immunizedanimals and stimulated with each of the respective compositions(peptides encoded in the minigene). The HTL response is measured using a³H-thymidine incorporation proliferation assay, (see, e.g., Alexander etal. Immunity 1:751-761, 1994). The results indicate the magnitude of theHTL response, thus demonstrating the in vivo immunogenicity of theminigene.

[0626] DNA minigenes, constructed as described in the previous Example,can also be confirmed as a vaccine in combination with a boosting agentusing a prime boost protocol. The boosting agent can consist ofrecombinant protein (e.g., Barnett et al., Aids Res. and HumanRetroviruses 14, Supplement 3:S299-S309, 1998) or recombinant vaccinia,for example, expressing a minigene or DNA encoding the complete proteinof interest (see, e.g., Hanke et al., Vaccine 16:439-445, 1998; Sedegahet al., Proc. Natl. Acad. Sci USA 95:7648-53, 1998; Hanke and McMichael,Immunol. Letters 66:177-181, 1999; and Robinson et al, Nature Med.5:526-34, 1999).

[0627] For example, the efficacy of the DNA minigene used in a primeboost protocol is initially evaluated in transgenic mice. In thisexample, A2.1/K^(b) transgenic mice are immunized IM with 100 μg of aDNA minigene encoding the immunogenic peptides including at least oneHLA-A2 supermotif-bearing peptide. After an incubation period (rangingfrom 3-9 weeks), the mice are boosted IP with 10⁷ pfu/mouse of arecombinant vaccinia virus expressing the same sequence encoded by theDNA minigene. Control mice are immunized with 100 μg of DNA orrecombinant vaccinia without the minigene sequence, or with DNA encodingthe minigene, but without the vaccinia boost. After an additionalincubation period of two weeks, splenocytes from the mice areimmediately assayed for peptide-specific activity in an ELISPOT assay.Additionally, splenocytes are stimulated in vitro with the A2-restrictedpeptide epitopes encoded in the minigene and recombinant vaccinia, thenassayed for peptide-specific activity in an alpha, beta and/or gamma IFNELISA.

[0628] It is found that the minigene utilized in a prime-boost protocolelicits greater immune responses toward the HLA-A2 supermotif peptidesthan with DNA alone. Such an analysis can also be performed using HLA-A11 or HLA-B7 transgenic mouse models to assess CTL induction by HLA-A3or HLA-B7 motif or supermotif epitopes. The use of prime boost protocolsin humans is described below in the Example entitled “Induction of CTLResponses Using a Prime Boost Protocol.”

Example 24 Peptide Compositions for Prophylactic Uses

[0629] Vaccine compositions of the present invention can be used toprevent 213P1F11 expression in persons who are at risk for tumors thatbear this antigen. For example, a polyepitopic peptide epitopecomposition (or a nucleic acid comprising the same) containing multipleCTL and HTL epitopes such as those selected in the above Examples, whichare also selected to target greater than 80% of the population, isadministered to individuals at risk for a 213P1F11-associated tumor.

[0630] For example, a peptide-based composition is provided as a singlepolypeptide that encompasses multiple epitopes. The vaccine is typicallyadministered in a physiological solution that comprises an adjuvant,such as Incomplete Freunds Adjuvant. The dose of peptide for the initialimmunization is from about 1 to about 50,000 μg, generally 100-5,000 μg,for a 70 kg patient. The initial administration of vaccine is followedby booster dosages at 4 weeks followed by evaluation of the magnitude ofthe immune response in the patient, by techniques that determine thepresence of epitope-specific CTL populations in a PBMC sample.Additional booster doses are administered as required. The compositionis found to be both safe and efficacious as a prophylaxis against213P1F11-associated disease.

[0631] Alternatively, a composition typically comprising transfectingagents is used for the administration of a nucleic acid-based vaccine inaccordance with methodologies known in the art and disclosed herein.

Example 25 Polyepitopic Vaccine Compositions Derived from Native213P1F11 Sequences

[0632] A native 213P1F11 polyprotein sequence is analyzed, preferablyusing computer algorithms defined for each class I and/or class IIsupermotif or motif, to identify “relatively short” regions of thepolyprotein that comprise multiple epitopes. The “relatively short”regions are preferably less in length than an entire native antigen.This relatively short sequence that contains multiple distinct oroverlapping, “nested” epitopes is selected; it can be used to generate aminigene construct. The construct is engineered to express the peptide,which corresponds to the native protein sequence. The “relatively short”peptide is generally less than 250 amino acids in length, often lessthan 100 amino acids in length, preferably less than 75 amino acids inlength, and more preferably less than 50 amino acids in length. Theprotein sequence of the vaccine composition is selected because it hasmaximal number of epitopes contained within the sequence, i.e., it has ahigh concentration of epitopes. As noted herein, epitope motifs may benested or overlapping (i.e., frame shifted relative to one another). Forexample, with overlapping epitopes, two 9-mer epitopes and one 10-merepitope can be present in a 10 amino acid peptide. Such a vaccinecomposition is administered for therapeutic or prophylactic purposes.

[0633] The vaccine composition will include, for example, multiple CTLepitopes from 213P1F11 antigen and at least one HTL epitope. Thispolyepitopic native sequence is administered either as a peptide or as anucleic acid sequence which encodes the peptide. Alternatively, ananalog can be made of this native sequence, whereby one or more of theepitopes comprise substitutions that alter the cross-reactivity and/orbinding affinity properties of the polyepitopic peptide.

[0634] The embodiment of this example provides for the possibility thatan as yet undiscovered aspect of immune system processing will apply tothe native nested sequence and thereby facilitate the production oftherapeutic or prophylactic immune response-inducing vaccinecompositions. Additionally such an embodiment provides for thepossibility of motif-bearing epitopes for an HLA makeup(s) that ispresently unknown. Furthermore, this embodiment (excluding an analogedembodiment) directs the immune response to multiple peptide sequencesthat are actually present in native 213P1F11, thus avoiding the need toevaluate any junctional epitopes. Lastly, the embodiment provides aneconomy of scale when producing peptide or nucleic acid vaccinecompositions.

[0635] Related to this embodiment, computer programs are available inthe art which can be used to identify in a target sequence, the greatestnumber of epitopes per sequence length.

Example 26 Polyepitopic Vaccine Compositions from Multiple Antigens

[0636] The 213P1F11 peptide epitopes of the present invention are usedin conjunction with epitopes from other target tumor-associatedantigens, to create a vaccine composition that is useful for theprevention or treatment of cancer that expresses 213P1F11 and such otherantigens. For example, a vaccine composition can be provided as a singlepolypeptide that incorporates multiple epitopes from 213P1F11 as well astumor-associated antigens that are often expressed with a target cancerassociated with 213P1F11 expression, or can be administered as acomposition comprising a cocktail of one or more discrete epitopes.Alternatively, the vaccine can be administered as a minigene constructor as dendritic cells which have been loaded with the peptide epitopesin vitro.

Example 27 Use of Peptides to Evaluate an Immune Response

[0637] Peptides of the invention may be used to analyze an immuneresponse for the presence of specific antibodies, CTL or HTL directed to213P1F11. Such an analysis can be performed in a manner described by Ogget al., Science 279:2103-2106, 1998. In this Example, peptides inaccordance with the invention are used as a reagent for diagnostic orprognostic purposes, not as an immunogen.

[0638] In this example highly sensitive human leukocyte antigentetrameric complexes (“tetramers”) are used for a cross-sectionalanalysis of, for example, 213P1F11 HLA-A*0201-specific CTL frequenciesfrom HLA A*0201-positive individuals at different stages of disease orfollowing immunization comprising a 213P1F11 peptide containing anA*0201 motif. Tetrameric complexes are synthesized as described (Museyet al., N. Engl J. Med. 337:1267, 1997). Briefly, purified HLA heavychain (A*0201 in this example) and P2-microglobulin are synthesized bymeans of a prokaryotic expression system. The heavy chain is modified bydeletion of the transmembrane-cytosolic tail and COOH-terminal additionof a sequence containing a BirA enzymatic biotinylation site. The heavychain, β2-microglobulin, and peptide are refolded by dilution. The 45-kDrefolded product is isolated by fast protein liquid chromatography andthen biotinylated by BirA in the presence of biotin (Sigma, St. Louis,Mo.), adenosine 5′ triphosphate and magnesium.Streptavidin-phycoerythrin conjugate is added in a 1:4 molar ratio, andthe tetrameric product is concentrated to 1 mg/ml. The resulting productis referred to as tetramer-phycoerythrin.

[0639] For the analysis of patient blood samples, approximately onemillion PBMCs are centrifuged at 300 g for 5 minutes and resuspended in50 μl of cold phosphate-buffered saline. Tri-color analysis is performedwith the tetramer-phycoerythrin, along with anti-CD8-Tricolor, andanti-CD38. The PBMCs are incubated with tetramer and antibodies on icefor 30 to 60 min and then washed twice before formaldehyde fixation.Gates are applied to contain >99.98% of control samples. Controls forthe tetramers include both A*0201-negative individuals andA*0201-positive non-diseased donors. The percentage of cells stainedwith the tetramer is then determined by flow cytometry. The resultsindicate the number of cells in the PBMC sample that containepitope-restricted CTLs, thereby readily indicating the extent of immuneresponse to the 213P1F11 epitope, and thus the status of exposure to213P1F11, or exposure to a vaccine that elicits a protective ortherapeutic response.

Example 28 Use of Peptide Epitopes to Evaluate Recall Responses

[0640] The peptide epitopes of the invention are used as reagents toevaluate T cell responses, such as acute or recall responses, inpatients. Such an analysis may be performed on patients who haverecovered from 213P1F11-associated disease or who have been vaccinatedwith a 213P1F11 vaccine.

[0641] For example, the class I restricted CTL response of persons whohave been vaccinated may be analyzed. The vaccine may be any 213P1F11vaccine. PBMC are collected from vaccinated individuals and HLA typed.Appropriate peptide epitopes of the invention that, optimally, bearsupermotifs to provide cross-reactivity with multiple HLA supertypefamily members, are then used for analysis of samples derived fromindividuals who bear that HLA type.

[0642] PBMC from vaccinated individuals are separated onFicoll-Histopaque density gradients (Sigma Chemical Co., St. Louis,Mo.), washed three times in HBSS (GIBCO Laboratories), resuspended inRPMI-1640 (GIBCO Laboratories) supplemented with L-glutamine (2 mM),penicillin (50U/ml), streptomycin (50 μg/ml), and Hepes (10 mM)containing 10% heat-inactivated human AB serum (complete RPMI) andplated using microculture formats. A synthetic peptide comprising anepitope of the invention is added at 10 μg/ml to each well and HBV core128-140 epitope is added at 1 μg/ml to each well as a source of T cellhelp during the first week of stimulation.

[0643] In the microculture format, 4×10⁵ PBMC are stimulated withpeptide in 8 replicate cultures in 96-well round bottom plate in 100μl/well of complete RPMI. On days 3 and 10, 100 μl of complete RPMI and20 U/ml final concentration of rIL-2 are added to each well. On day 7the cultures are transferred into a 96-well flat-bottom plate andrestimulated with peptide, rIL-2 and 105 irradiated (3,000 rad)autologous feeder cells. The cultures are tested for cytotoxic activityon day 14. A positive CTL response requires two or more of the eightreplicate cultures to display greater than 10% specific ⁵¹Cr release,based on comparison with non-diseased control subjects as previouslydescribed (Rehermann, et al, Nature Med. 2:1104,1108, 1996; Rehermann etal, J. Clin. Invest. 97:1655-1665, 1996; and Rehermann et al J. Clin.Invest. 98:1432-1440, 1996).

[0644] Target cell lines are autologous and allogeneic EBV-transformedB-LCL that are either purchased from the American Society forHistocompatibility and Immunogenetics (ASHI, Boston, Mass.) orestablished from the pool of patients as described (Guilhot, et al J.Virol. 66:2670-2678, 1992).

[0645] Cytotoxicity assays are performed in the following manner. Targetcells consist of either allogeneic HLA-matched or autologousEBV-transformed B lymphoblastoid cell line that are incubated overnightwith the synthetic peptide epitope of the invention at 10 μM, andlabeled with 100 μCi of ⁵¹Cr (Amersham Corp., Arlington Heights, Ill.)for 1 hour after which they are washed four times with HBSS.

[0646] Cytolytic activity is determined in a standard 4-h, split well⁵¹Cr release assay using U-bottomed 96 well plates containing 3,000targets/well. Stimulated PBMC are tested at effector/target (E/T) ratiosof 20-50:1 on day 14. Percent cytotoxicity is determined from theformula: 100×[(experimental release-spontaneous release)/maximumrelease-spontaneous release)]. Maximum release is determined by lysis oftargets by detergent (2% Triton X-100; Sigma Chemical Co., St. Louis,Mo.). Spontaneous release is <25% of maximum release for allexperiments.

[0647] The results of such an analysis indicate the extent to whichHLA-restricted CTL populations have been stimulated by previous exposureto 213P1F11 or a 213P1F11 vaccine.

[0648] Similarly, Class II restricted HTL responses may also beanalyzed. Purified PBMC are cultured in a 96-well flat bottom plate at adensity of 1.5×10⁵ cells/well and are stimulated with 10 μg/ml syntheticpeptide of the invention, whole 213P1F11 antigen, or PHA. Cells areroutinely plated in replicates of 4-6 wells for each condition. Afterseven days of culture, the medium is removed and replaced with freshmedium containing 10U/ml IL-2. Two days later, 1 μCi ³H-thymidine isadded to each well and incubation is continued for an additional 18hours. Cellular DNA is then harvested on glass fiber mats and analyzedfor ³H-thymidine incorporation. Antigen-specific T cell proliferation iscalculated as the ratio of ³H-thymidine incorporation in the presence ofantigen divided by the ³H-thymidine incorporation in the absence ofantigen.

Example 29 Induction of Specific CTL Response in Humans

[0649] A human clinical trial for an immunogenic composition comprisingCTL and HTL epitopes of the invention is set up as an IND Phase I, doseescalation study and carried out as a randomized, double-blind,placebo-controlled trial. Such a trial is designed, for example, asfollows:

[0650] A total of about 27 individuals are enrolled and divided into 3groups:

[0651] Group I: 3 subjects are injected with placebo and 6 subjects areinjected with 5 μg of peptide composition;

[0652] Group II: 3 subjects are injected with placebo and 6 subjects areinjected with 50 μg peptide composition;

[0653] Group III: 3 subjects are injected with placebo and 6 subjectsare injected with 500 μg of peptide composition.

[0654] After 4 weeks following the first injection, all subjects receivea booster inoculation at the same dosage.

[0655] The endpoints measured in this study relate to the safety andtolerability of the peptide composition as well as its immunogenicity.Cellular immune responses to the peptide composition are an index of theintrinsic activity of this the peptide composition, and can therefore beviewed as a measure of biological efficacy. The following summarize theclinical and laboratory data that relate to safety and efficacyendpoints.

[0656] Safety: The incidence of adverse events is monitored in theplacebo and drug treatment group and assessed in terms of degree andreversibility.

[0657] Evaluation of Vaccine Efficacy: For evaluation of vaccineefficacy, subjects are bled before and after injection. Peripheral bloodmononuclear cells are isolated from fresh heparinized blood byFicoll-Hypaque density gradient centrifugation, aliquoted in freezingmedia and stored frozen. Samples are assayed for CTL and HTL activity.

[0658] The vaccine is found to be both safe and efficacious.

Example 30 Phase II Trials in Patients Expressing 213P1F11

[0659] Phase II trials are performed to study the effect ofadministering the CTL-HTL peptide compositions to patients having cancerthat expresses 213P1F11. The main objectives of the trial are todetermine an effective dose and regimen for inducing CTLs in cancerpatients that express 213P1F11, to establish the safety of inducing aCTL and HTL response in these patients, and to see to what extentactivation of CTLs improves the clinical picture of these patients, asmanifested, e.g., by the reduction and/or shrinking of lesions. Such astudy is designed, for example, as follows:

[0660] The studies are performed in multiple centers. The trial designis an open-label, uncontrolled, dose escalation protocol wherein thepeptide composition is administered as a single dose followed six weekslater by a single booster shot of the same dose. The dosages are 50, 500and 5,000 micrograms per injection. Drug-associated adverse effects(severity and reversibility) are recorded.

[0661] There are three patient groupings. The first group is injectedwith 50 micrograms of the peptide composition and the second and thirdgroups with 500 and 5,000 micrograms of peptide composition,respectively. The patients within each group range in age from 21-65 andrepresent diverse ethnic backgrounds. All of them have a tumor thatexpresses 213P1F11.

[0662] Clinical manifestations or antigen-specific T-cell responses aremonitored to assess the effects of administering the peptidecompositions. The vaccine composition is found to be both safe andefficacious in the treatment of 213P1F11-associated disease.

Example 31 Induction of CTL Responses Using a Prime Boost Protocol

[0663] A prime boost protocol similar in its underlying principle tothat used to confirm the efficacy of a DNA vaccine in transgenic mice,such as described above in the Example entitled “The Plasmid Constructand the Degree to Which It Induces Immunogenicity,” can also be used forthe administration of the vaccine to humans. Such a vaccine regimen caninclude an initial administration of, for example, naked DNA followed bya boost using recombinant virus encoding the vaccine, or recombinantprotein/polypeptide or a peptide mixture administered in an adjuvant.

[0664] For example, the initial immunization may be performed using anexpression vector, such as that constructed in the Example entitled“Construction of “Minigene” Multi-Epitope DNA Plasmids” in the form ofnaked nucleic acid administered IM (or SC or ID) in the amounts of 0.5-5mg at multiple sites. The nucleic acid (0.1 to 1000 μg) can also beadministered using a gene gun. Following an incubation period of 3-4weeks, a booster dose is then administered. The booster can berecombinant fowlpox virus administered at a dose of 5-10⁷ to 5×10⁹ pfu.An alternative recombinant virus, such as an MVA, canarypox, adenovirus,or adeno-associated virus, can also be used for the booster, or thepolyepitopic protein or a mixture of the peptides can be administered.For evaluation of vaccine efficacy, patient blood samples are obtainedbefore immunization as well as at intervals following administration ofthe initial vaccine and booster doses of the vaccine. Peripheral bloodmononuclear cells are isolated from fresh heparinized blood byFicoll-Hypaque density gradient centrifugation, aliquoted in freezingmedia and stored frozen. Samples are assayed for CTL and HTL activity.

[0665] Analysis of the results indicates that a magnitude of responsesufficient to achieve a therapeutic or protective immunity against213P1F11 is generated.

Example 32 Administration of Vaccine Compositions Using Dendritic Cells(DC)

[0666] Vaccines comprising peptide epitopes of the invention can beadministered using APCs, or “professional” APCs such as DC. In thisexample, peptide-pulsed DC are administered to a patient to stimulate aCTL response in vivo. In this method, dendritic cells are isolated,expanded, and pulsed with a vaccine comprising peptide CTL and HTLepitopes of the invention. The dendritic cells are infused back into thepatient to elicit CTL and HTL responses in vivo. The induced CTL and HTLthen destroy or facilitate destruction, respectively, of the targetcells that bear the 213P1F11 protein from which the epitopes in thevaccine are derived.

[0667] For example, a cocktail of epitope-comprising peptides isadministered ex vivo to PBMC, or isolated DC therefrom. A pharmaceuticalto facilitate harvesting of DC can be used, such as Progenipoietin™(Monsanto, St. Louis, Mo.) or GM-CSF/IL-4. After pulsing the DC withpeptides, and prior to reinfusion into patients, the DC are washed toremove unbound peptides.

[0668] As appreciated clinically, and readily determined by one of skillbased on clinical outcomes, the number of DC reinfused into the patientcan vary (see, e.g., Nature Med. 4:328, 1998; Nature Med. 2:52, 1996 andProstate 32:272, 1997). Although 2-50×10⁶ DC per patient are typicallyadministered, larger number of DC, such as 10⁷ or 10⁸ can also beprovided. Such cell populations typically contain between 50-90% DC.

[0669] In some embodiments, peptide-loaded PBMC are injected intopatients without purification of the DC. For example, PBMC generatedafter treatment with an agent such as Progenipoietin™ are injected intopatients without purification of the DC. The total number of PBMC thatare administered often ranges from 10⁸ to 10¹⁰. Generally, the celldoses injected into patients is based on the percentage of DC in theblood of each patient, as determined, for example, by immunofluorescenceanalysis with specific anti-DC antibodies. Thus, for example, ifProgenipoietin™ mobilizes 2% DC in the peripheral blood of a givenpatient, and that patient is to receive 5×10⁶ DC, then the patient willbe injected with a total of 2.5×10⁸ peptide-loaded PBMC. The percent DCmobilized by an agent such as Progenipoietin™ is typically estimated tobe between 2-10%, but can vary as appreciated by one of skill in theart.

[0670] Ex vivo activation of CTL/HTL responses Alternatively, ex vivoCTL or HTL responses to 213P1F11 antigens can be induced by incubating,in tissue culture, the patient's, or genetically compatible, CTL or HTLprecursor cells together with a source of APC, such as DC, andimmunogenic peptides. After an appropriate incubation time (typicallyabout 7-28 days), in which the precursor cells are activated andexpanded into effector cells, the cells are infused into the patient,where they will destroy (CTL) or facilitate destruction (HTL) of theirspecific target cells, i.e., tumor cells.

Example 33 An Alternative Method of Identifying and ConfirmingMotif-Bearing Peptides

[0671] Another method of identifying and confirming motif-bearingpeptides is to elute them from cells bearing defined MHC molecules. Forexample, EBV transformed B cell lines used for tissue typing have beenextensively characterized to determine which HLA molecules they express.In certain cases these cells express only a single type of HLA molecule.These cells can be transfected with nucleic acids that express theantigen of interest, e.g. 213P1F11. Peptides produced by endogenousantigen processing of peptides produced as a result of transfection willthen bind to HLA molecules within the cell and be transported anddisplayed on the cell's surface. Peptides are then eluted from the HLAmolecules by exposure to mild acid conditions and their amino acidsequence determined, e.g., by mass spectral analysis (e.g., Kubo et al.,J. Immunol. 152:3913, 1994). Because the majority of peptides that binda particular HLA molecule are motif-bearing, this is an alternativemodality for obtaining the motif-bearing peptides correlated with theparticular HLA molecule expressed on the cell.

[0672] Alternatively, cell lines that do not express endogenous HLAmolecules can be transfected with an expression construct encoding asingle HLA allele. These cells can then be used as described, i.e., theycan then be transfected with nucleic acids that encode 213P1F11 toisolate peptides corresponding to 213P1F11 that have been presented onthe cell surface. Peptides obtained from such an analysis will bearmotif(s) that correspond to binding to the single HLA allele that isexpressed in the cell.

[0673] As appreciated by one in the art, one can perform a similaranalysis on a cell bearing more than one HLA allele and subsequentlydetermine peptides specific for each HLA allele expressed. Moreover, oneof skill would also recognize that means other than transfection, suchas loading with a protein antigen, can be used to provide a source ofantigen to the cell.

Example 34 Complementary Polynucleotides

[0674] Sequences complementary to the 213P1F11-encoding sequences, orany parts thereof, are used to detect, decrease, or inhibit expressionof naturally occurring 213P1F11. Although use of oligonucleotidescomprising from about 15 to 30 base pairs is described, essentially thesame procedure is used with smaller or with larger sequence fragments.Appropriate oligonucleotides are designed using, e.g., OLIGO 4.06software (National Biosciences) and the coding sequence of 213P1F11. Toinhibit transcription, a complementary oligonucleotide is designed fromthe most unique 5′ sequence and used to prevent promoter binding to thecoding sequence. To inhibit translation, a complementary oligonucleotideis designed to prevent ribosomal binding to a 213P1F11-encodingtranscript.

Example 35 Purification of Naturally-Occurring or Recombinant 213P1F11Using 213P1F11-Specific Antibodies

[0675] Naturally occurring or recombinant 213P1F11 is substantiallypurified by immunoaffinity chromatography using antibodies specific for213P1F11. An immunoaffinity column is constructed by covalently couplinganti-213P1F11 antibody to an activated chromatographic resin, such asCNBr-activated SEPFIAROSE (Amersham Pharmacia Biotech). After thecoupling, the resin is blocked and washed according to themanufacturer's instructions.

[0676] Media containing 213P1F11 are passed over the immunoaffinitycolumn, and the column is washed under conditions that allow thepreferential absorbance of 213P1F11 (e.g., high ionic strength buffersin the presence of detergent). The column is eluted under conditionsthat disrupt antibody/213P1F11 binding (e.g., a buffer of pH 2 to pH 3,or a high concentration of a chaotrope, such as urea or thiocyanateion), and GCR.P is collected.

Example 36 Identification of Molecules Which Interact with 213P1F11

[0677] 213P1F11, or biologically active fragments thereof, are labeledwith 121 1 Bolton-Hunter reagent. (See, e.g., Bolton et al. (1973)Biochem. J. 133:529.) Candidate molecules previously arrayed in thewells of a multi-well plate are incubated with the labeled 213P1F11,washed, and any wells with labeled 213P1F11 complex are assayed. Dataobtained using different concentrations of 213P1F11 are used tocalculate values for the number, affinity, and association of 213P1F11with the candidate molecules.

Example 37 In Vivo Assay for 213P1F11 Tumor Growth Promotion

[0678] The effect of the 213P1F11 protein on tumor cell growth isevaluated in vivo by evaluating tumor development and growth of cellsexpressing or lacking 213P1F11. For example, SCID mice are injectedsubcutaneously on each flank with 1×10⁶ of either prostate, bladder orbreast cancer cell lines (such as PC3, DU145, UM-UC3, J82, MCF7) orN1H-3T3 cells containing tkNeo empty vector or 213P1F11. At least twostrategies may be used: (1) Constitutive 213P1F11 expression underregulation of a promoter such as a constitutive promoter obtained fromthe genomes of viruses such as polyoma virus, fowlpox virus (UK2,211,504 published Jul. 5, 1989), adenovirus (such as Adenovirus 2),bovine papilloma virus, avian sarcoma virus, cytomegalovirus, aretrovirus, hepatitis-B virus and Simian Virus 40 (SV40), or fromheterologous mammalian promoters, e.g., the actin promoter or animmunoglobulin promoter, provided such promoters are compatible with thehost cell systems, and (2) Regulated expression under control of aninducible vector system, such as ecdysone, tet, etc., provided suchpromoters are compatible with the host cell systems. Tumor volume isthen monitored at the appearance of palpable tumors and followed overtime to determine if 213P1F11-expressing cells grow at a faster rate andwhether tumors produced by 213P1F11-expressing cells demonstratecharacteristics of altered aggressiveness (e.g. enhanced metastasis,vascularization, reduced responsiveness to chemotherapeutic drugs).

[0679] Additionally, mice can be implanted with 1×105 of the same cellsorthotopically to determine if 213P1F11 has an effect on local growth inthe prostate or on the ability of the cells to metastasize, specificallyto lungs, lymph nodes, and bone marrow.

[0680] The assay is also useful to determine the 213P1F11 inhibitoryeffect of candidate therapeutic compositions, such as for example,213P1F11 intrabodies, 213P1F11 antisense molecules and ribozymes.

Example 38 213P1F11 Monoclonal Antibody-mediated Inhibition of Tumors InVivo

[0681] The significant expression of 213P1F11 in cancer tissues,together with its restricted expression in normal tissues, makes213P1F11 an excellent target for antibody therapy. In cases where themonoclonal antibody target is a cell surface protein, antibodies havebeen shown to be efficacious at inhibiting tumor growth (See, e.g.,(Saffran, D., et al., PNAS 10: 1073-1078 orwww.pnas.org/cgi/doi/10.1073/pnas.051624698). In cases where the targetis not on the cell surface, such as for 213P1F11 and including PSA andPAP in prostate cancer, antibodies have still been shown to recognizeand inhibit growth of cells expressing those proteins (Saffran, D. C.,et al., Cancer and Metastasis Reviews, 1999. 18: p. 437-449). As withany cellular protein with a restricted expression profile, 213P1F11 is atarget for T cell-based immunotherapy.

[0682] Accordingly, the therapeutic efficacy of anti-213P1F11 mAbs inhuman prostate, bladder and breast cancer mouse models is investigatedusing in 213P1F11-expressing prostate and bladder cancer xenografts aswell as prostate, bladder and breast cancer cell lines, such as thosedescribed in the Example entitled “In Vivo Assay for 213P1F11 TumorGrowth Promotion,” that have been engineered to express 213P1F11.

[0683] Antibody efficacy on tumor growth and metastasis formation isconfirmed, e.g., in a mouse orthotopic prostate or bladder cancerxenograft models, as well as SCID mice injected with prostate, bladderand breast cancer cell lines, such as those described in the Exampleentitled “In Vivo Assay for 213P1F11 Tumor Growth Promotion,” designedto express or lack 213P1F11. Therapeutic efficacy of anti-213P1F11 mAbsin prostate cancer is also evaluated in human prostate xenograft mousemodels such as the LAPC-9 xenografts (Craft, N., et al.,. Cancer Res,1999. 59(19): p. 5030-6). The antibodies can be unconjugated, asdiscussed in this Example, or can be conjugated to a therapeuticmodality, as appreciated in the art. It is confirmed that anti-213P1F11mabs inhibit formation of 213P1F11-expressing tumors. Anti-213P1F11 mAbsinhibit formation of the androgen-independent LAPC-9-AI tumorxenografts, as well as PC3-213P1F11, MCF7-213P1F11 and UM-UC3-213P1F11tumors. Anti-213P1F11 mAbs also retard the growth of establishedorthotopic tumors and prolong survival of tumor-bearing mice. Theseresults indicate the utility of anti-213P1F11 mAbs in the treatment oflocal and advanced stages of prostate, bladder or breast cancer. (See,e.g., Saffran, D., et al., PNAS 10:1073-1078 or www.pnas.org/cgi/doi/10.1073/pnas.051624698)

[0684] Administration of anti-213P1F11 mAbs retard establishedorthotopic tumor growth and inhibit metastasis to distant sites,resulting in a significant prolongation in the survival of tumor-bearingmice. These studies indicate that 213P1F11 is an attractive target forimmunotherapy and demonstrate the therapeutic potential of anti-213P1F11mAbs for the treatment of local and metastatic bladder cancer.

[0685] This example demonstrates that unconjugated 213P1F11 monoclonalantibodies effectively to inhibit the growth of human prostate, bladderand breast tumors grown in SCID mice; accordingly a combination of suchefficacious monoclonal antibodies is also effective.

[0686] Tumor Inhibition Using Multiple Unconjugated 213P1F11 mAbs

[0687] Materials and Methods

[0688] 213P1F11 Monoclonal Antibodies:

[0689] Monoclonal antibodies are raised against 213P1F11 as described inthe Example entitled “Generation of 213P1F11 Monoclonal Antibodies(mAbs).” The antibodies are characterized by ELISA, Western blot, FACS,and immunoprecipitation, in accordance with techniques known in the art,for their capacity to bind 213P1F11. Epitope mapping data for theanti-213P1F11 mAbs, as determined by ELISA and Western analysis,recognize epitopes on the 213P1F11 protein. Immunohistochemical analysisof bladder cancer tissues and cells with these antibodies is performed.

[0690] The monoclonal antibodies are purified from ascites or hybridomatissue culture supernatants by Protein-G Sepharose chromatography,dialyzed against PBS, filter sterilized, and stored at −20° C. Proteindeterminations are performed by a Bradford assay (Bio-Rad, Hercules,Calif.). A therapeutic monoclonal antibody or a cocktail comprising amixture of individual monoclonal antibodies is prepared and used for thetreatment of mice receiving subcutaneous or orthotopic injections ofbladder tumor xenografts.

[0691] Cancer Xenograft and Cell Lines

[0692] The LAPC-9 xenograft, which expresses a wild-type androgenreceptor and produces prostate-specific antigen (PSA), is passaged in 6-to 8-week-old male ICR-severe combined immunodeficient (SCID) mice(Taconic Farns) by s.c. trocar implant (Craft, N., et al., supra).Prostate, bladder or breast cancer cell lines (such as PC3, DU145,UM-UC3, J82, MCF7) expressing 213P1F11 are generated by retroviral genetransfer as described in Hubert, R. S., et al., STEAP: aprostate-specific cell-surface antigen highly expressed in humanprostate tumors. Proc Natl Acad Sci USA, 1999. 96(25):14523-8.Anti-213P1F11 staining is detected by using an FITC-conjugated goatanti-mouse antibody (Southern Biotechnology Associates) followed byanalysis on a Coulter Epics-XL f low cytometer.

[0693] In Vivo Mouse Models.

[0694] Subcutaneous (s.c.) tumors are generated by injection of 1×10⁶213P1F11-expressing cancer cells mixed at a 1:1 dilution with Matrigel(Collaborative Research) in the right flank of male SCID mice. To testantibody efficacy on tumor formation, i.p. antibody injections arestarted on the same day as tumor-cell injections. As a control, mice areinjected with either purified mouse IgG (ICN) or PBS; or a purifiedmonoclonal antibody that recognizes an irrelevant antigen not expressedin human cells. In preliminary studies, no difference is found betweenmouse IgG or PBS on tumor growth. Tumor sizes are determined by verniercaliper measurements, and the tumor volume is calculated aslength×width×height. Mice with s.c. tumors greater than 1.5 cm indiameter are sacrificed. Circulating levels of anti-213P1F11 Abs aredetermined by a capture ELISA kit (Bethyl Laboratories, Montgomery,Tex.). (See, e.g., (Saffran, D., et al., PNAS 10:1073-1078)

[0695] Orthotopic injections are performed, for example, in twoalternative embodiments, under anesthesia by, for example, use ofketamine/xylazine. In a first embodiment, an intravesicular injection ofbladder cancer cells is administered directly through the urethra andinto the bladder (Peralta, E. A., et al., J. Urol., 1999.162:1806-1811). In a second embodiment, an incision is made through theabdominal wall, the bladder is exposed, and bladder tumor tissue pieces(1-2 mm in size) derived from a s.c. tumor are surgically glued onto theexterior wall of the bladder, termed “onplantation” (Fu, X., et al.,Int. J. Cancer, 1991. 49: 938-939; Chang, S., et al., Anticancer Res.,1997. 17: p.3239-3242). For prostate orthotopic studies, an incision ismade through the abdominal muscles to expose the bladder and seminalvesicles, which then are delivered through the incision to the exposedthe dorsal prostate. Antibodies can be administered to groups of mice atthe time of tumor injection or onplantation, or after 1-2 weeks to allowtumor establishment.

[0696] Anti-213P1F11 mAbs Inhibit Growth of 213P1F11-Expressing CancerTumors

[0697] In one embodiment, the effect of anti-213P1F11 mAbs on tumorformation is tested by using the prostate and bladder orthotopic models.As compared with the s.c. tumor model, the orthotopic model, whichrequires surgical attachment of tumor tissue directly on the prostate orbladder, results in a local tumor growth, development of metastasis indistal sites, and subsequent death (Fu, X., et al., Int. J. Cancer,1991. 49: p. 938-939; Chang, S., et al., Anticancer Res., 1997. 17: p.3239-3242). This feature make the orthotopic model more representativeof human disease progression and allows one to follow the therapeuticeffect of mAbs, as well as other therapeutic modalities, on clinicallyrelevant end points.

[0698] Accordingly, 213P1F11-expressing tumor cells are implantedorthotopically, and 2 days later, the mice are segregated into twogroups and treated with either: a) 50-2000 μg, usually 200-500 μg, ofanti-213P1F11 Ab, or b) PBS, three times per week for two to five weeks.Mice are monitored weekly for indications of tumor growth.

[0699] As noted, a major advantage of the orthotopic prostate andbladder cancer models is the ability to study the development ofmetastases. Formation of metastasis in mice bearing establishedorthotopic tumors is studied by histological analysis of tissuesections, including lung and lymph nodes (Fu, X., et al., Int. J.Cancer, 1991. 49:938-939; Chang, S., et al., Anticancer Res., 1997.17:3239-3242). Additionally, 1HC analysis using anti-213P1F11 antibodiescan be performed on the tissue sections.

[0700] Mice bearing established orthotopic 213P1F11-expressing tumorsare administered 1000 μg injections of either anti-213P1F11 mAb or PBSover a 4-week period. Mice in both groups are allowed to establish ahigh tumor burden (1-2 weeks growth), to ensure a high frequency ofmetastasis formation in mouse lungs and lymph nodes. Mice are thensacrificed and their local bladder tumor and lung and lymph node tissueare analyzed for the presence of tumor cells by histology and IHCanalysis.

[0701] These studies demonstrate a broad anti-tumor efficacy ofanti-213P1F11 antibodies on initiation and progression of bladder cancerin mouse models. Anti-213P1F11 antibodies inhibit tumor formation andretard the growth of already established tumors and prolong the survivalof treated mice. Moreover, anti-213P1F11 mAbs demonstrate a dramaticinhibitory effect on the spread of local prostate, bladder and breasttumors to distal sites, even in the presence of a large tumor burden.Thus, anti-213P1F11 mAbs are efficacious on major clinically relevantend points including lessened tumor growth, lessened metastasis, andprolongation of survival.

Example 39 Therapeutic and Diagnostic use of Anti-213P1F11 Antibodies inHumans

[0702] Anti-213P1F11 monoclonal antibodies are safely and effectivelyused for diagnostic, prophylactic, prognostic and/or therapeuticpurposes in humans. Western blot and immunohistochemical analysis ofcancer tissues and cancer xenografts with anti-213P1F11 mAb show strongextensive staining in carcinoma but significantly lower or undetectablelevels in normal tissues. Detection of 213P1F11 in carcinoma and inmetastatic disease demonstrates the usefulness of the mAb as adiagnostic and/or prognostic indicator. Anti-213P1F11 antibodies aretherefore used in diagnostic applications such as immunohistochemistryof kidney biopsy specimens to detect cancer from suspect patients.

[0703] As determined by flow cytometry, anti-213P1F11 mAb specificallybinds to carcinoma cells. Thus, anti-213P1F11 antibodies are used indiagnostic whole body imaging applications, such asradioinmrunoscintigraphy and radioimmunotherapy, (see, e.g., PotamianosS., et. al. Anticancer Res 20(2A):925-948 (2000)) for the detection oflocalized and metastatic cancers that exhibit expression of 213P1F11.Shedding or release of an extracellular domain of 213P1F11 into theextracellular milieu, such as that seen for alkaline phosphodiesteraseB10 (Meerson, N. R., Hepatology 27:563-568 (1998)), allows diagnosticdetection of 213P1F11 by anti-213P1F11 antibodies in serum and/or urinesamples from suspect patients.

[0704] Anti-213P1F11 antibodies that specifically bind 213P1F11 are usedin therapeutic applications for the treatment of cancers that express213P1F11. Anti-213P1F11 antibodies are used as an unconjugated modalityand as conjugated form in which the antibodies are attached to one ofvarious therapeutic or imaging modalities well known in the art, such asa prodrugs, enzymes or radioisotopes. In preclinical studies,unconjugated and conjugated anti-213P1F11 antibodies are tested forefficacy of tumor prevention and growth inhibition in the SCID mousecancer xenograft models, e.g., kidney cancer models AGS-K3 and AGS-K6,(see, e.g., the Example entitled “213P1F11 Monoclonal Antibody-mediatedInhibition of Bladder and Lung Tumors In Vivo”). Conjugated andunconjugated anti-213P1F11 antibodies are used as a therapeutic modalityin human clinical trials either alone or in combination with othertreatments as described in following Examples.

Example 40 Human Clinical Trials for the Treatment and Diagnosis ofHuman Carcinomas through use of Human Anti-213P1F11 Antibodies In Vivo

[0705] Antibodies are used in accordance with the present inventionwhich recognize an epitope on 213P1F11, and are used in the treatment ofcertain tumors such as those listed in Table I. Based upon a number offactors, including 213P1F11 expression levels, tumors such as thoselisted in Table I are presently preferred indications. In connectionwith each of these indications, three clinical approaches aresuccessfully pursued.

[0706] I.) Adjunctive therapy: In adjunctive therapy, patients aretreated with anti-213P1F11 antibodies in combination with achemotherapeutic or antineoplastic agent and/or radiation therapy.Primary cancer targets, such as those listed in Table I, are treatedunder standard protocols by the addition anti-213P1F11 antibodies tostandard first and second line therapy. Protocol designs addresseffectiveness as assessed by reduction in tumor mass as well as theability to reduce usual doses of standard chemotherapy. These dosagereductions allow additional and/or prolonged therapy by reducingdose-related toxicity of the chemotherapeutic agent. Anti-213P1F11antibodies are utilized in several adjunctive clinical trials incombination with the chemotherapeutic or antineoplastic agentsadriamycin (advanced prostrate carcinoma), cisplatin (advanced head andneck and lung carcinomas), taxol (breast cancer), and doxorubicin(preclinical).

[0707] II.) Monotherapy: In connection with the use of the anti-213P1F11antibodies in monotherapy of tumors, the antibodies are administered topatients without a chemotherapeutic or antineoplastic agent. In oneembodiment, monotherapy is conducted clinically in end stage cancerpatients with extensive metastatic disease. Patients show some diseasestabilization. Trials demonstrate an effect in refractory patients withcancerous tumors.

[0708] III.) Imaging Agent: Through binding a radionuclide (e.g., iodineor yttrium (I¹³¹, Y⁹⁰) to anti-213P1F11 antibodies, the radiolabeledantibodies are utilized as a diagnostic and/or imaging agent. In such arole, the labeled antibodies localize to both solid tumors, as well as,metastatic lesions of cells expressing 213P1F11. In connection with theuse of the anti-213P1F11 antibodies as imaging agents, the antibodiesare used as an adjunct to surgical treatment of solid tumors, as both apre-surgical screen as well as a post-operative follow-up to determinewhat tumor remains and/or returns. In one embodiment, a (¹¹¹In)-213P1F11antibody is used as an imaging agent in a Phase I human clinical trialin patients having a carcinoma that expresses 213P1F11 (by analogy see,e.g., Divgi et al. J. Natl Cancer Inst. 83:97-104 (1991)). Patients arefollowed with standard anterior and posterior gamma camera. The resultsindicate that primary lesions and metastatic lesions are identified

[0709] Dose and Route of Administration

[0710] As appreciated by those of ordinary skill in the art, dosingconsiderations can be determined through comparison with the analogousproducts that are in the clinic. Thus, anti-213P1F11 antibodies can beadministered with doses in the range of 5 to 400 mg/m², with the lowerdoses used, e.g., in connection with safety studies. The affinity ofanti-213P1F11 antibodies relative to the affinity of a known antibodyfor its target is one parameter used by those of skill in the art fordetermining analogous dose regimens. Further, anti-213P1F11 antibodiesthat are fully human antibodies, as compared to the chimeric antibody,have slower clearance; accordingly, dosing in patients with such fullyhuman anti-213P1F11 antibodies can be lower, perhaps in the range of 50to 300 mg/m ², and still remain efficacious. Dosing in mg/m², as opposedto the conventional measurement of dose in mg/kg, is a measurement basedon surface area and is a convenient dosing measurement that is designedto include patients of all sizes from infants to adults.

[0711] Three distinct delivery approaches are useful for delivery ofanti-213P1F11 antibodies. Conventional intravenous delivery is onestandard delivery technique for many tumors. However, in connection withtumors in the peritoneal cavity, such as tumors of the ovaries, biliaryduct, other ducts, and the like, intraperitoneal administration mayprove favorable for obtaining high dose of antibody at the tumor and toalso minimize antibody clearance. In a similar manner, certain solidtumors possess vasculature that is appropriate for regional perfusion.Regional perfusion allows for a high dose of antibody at the site of atumor and minimizes short term clearance of the antibody.

[0712] Clinical Development Plan (CDP)

[0713] Overview: The CDP follows and develops treatments ofanti-213P1F11 antibodies in connection with adjunctive therapy,monotherapy, and as an imaging agent. Trials initially demonstratesafety and thereafter confirm efficacy in repeat doses. Trails are openlabel comparing standard chemotherapy with standard therapy plusanti-213P1F11 antibodies. As will be appreciated, one criteria that canbe utilized in connection with enrollment of patients is 213P1F11expression levels in their tumors as determined by biopsy.

[0714] As with any protein or antibody infusion-based therapeutic,safety concerns are related primarily to (i) cytokine release syndrome,i.e., hypotension, fever, shaking, chills; (ii) the development of animmunogenic response to the material (i.e., development of humanantibodies by the patient to the antibody therapeutic, or HAMAresponse); and, (iii) toxicity to normal cells that express 213P1F11.Standard tests and follow-up are utilized to monitor each of thesesafety concerns. Anti-213P1F11 antibodies are found to be safe uponhuman administration.

Example 41 Human Clinical Trial Adjunctive Therapy with HumanAnti-213P1F11 Antibody and Chemotherapeutic Agent

[0715] A phase I human clinical trial is initiated to assess the safetyof six intravenous doses of a human anti-213P1F11 antibody in connectionwith the treatment of a solid tumor, e.g., a cancer of a tissue listedin Table I. In the study, the safety of single doses of anti-213P1F11antibodies when utilized as an adjunctive therapy to an antineoplasticor chemotherapeutic agent, such as cisplatin, topotecan, doxorubicin,adriamycin, taxol, or the like, is assessed. The trial design includesdelivery of six single doses of an anti-213P1F11 antibody with dosage ofantibody escalating from approximately about 25 mg/m² to about 275 mg/²over the course of the treatment in accordance with the followingschedule: Day 0 Day 7 Day 14 Day 21 Day 28 Day 35 mAb Dose 25 75 125 175225 275 mg/m² mg/m² mg/m² mg/m² mg/m² mg/m² Chemotherapy + + + + + +(standard dose)

[0716] Patients are closely followed for one-week following eachadministration of antibody and chemotherapy. In particular, patients areassessed for the safety concerns mentioned above: (i) cytokine releasesyndrome, i.e., hypotension, fever, shaking, chills; (ii) thedevelopment of an immunogenic response to the material (i.e.,development of human antibodies by the patient to the human antibodytherapeutic, or HAHA response); and, (iii) toxicity to normal cells thatexpress 213P1F11. Standard tests and follow-up are utilized to monitoreach of these safety concerns. Patients are also assessed for clinicaloutcome, and particularly reduction in tumor mass as evidenced by MRI orother imaging.

[0717] The anti-213P1F11 antibodies are demonstrated to be safe andefficacious, Phase II trials confirm the efficacy and refine optimumdosing.

Example 42 Human Clinical Trial: Monotherapy with Human Anti-213P1F11Antibody

[0718] Anti-213P11F11 antibodies are safe in connection with theabove-discussed adjunctive trial, a Phase II human clinical trialconfirms the efficacy and optimum dosing for monotherapy. Such trial isaccomplished, and entails the same safety and outcome analyses, to theabove-described adjunctive trial with the exception being that patientsdo not receive chemotherapy concurrently with the receipt of doses ofanti-213P1F11 antibodies.

Example 43 Human Clinical Trial: Diagnostic Imaging with Anti-213P1F11Antibody

[0719] Once again, as the adjunctive therapy discussed above is safewithin the safety criteria discussed above, a human clinical trial isconducted concerning the use of anti-213P1F11 antibodies as a diagnosticimaging agent. The protocol is designed in a substantially similarmanner to those described in the art, such as in Divgi et al. J. Natl.Cancer Inst. 83:97-104 (1991). The antibodies are found to be both safeand efficacious when used as a diagnostic modality.

Example 44 Homology Comparison of 213P1F11 to Known Sequences

[0720] The 213P1F11 gene is homologous to a previously cloned gene,namely the human caspase 14 precursor (gi 6912286) (Hu S et al, J. Biol.Chem. 1998, 273:29648), also known as mini-ICE (MICE). The 213P1F11 generesulted in several protein variants, which share severalcharacteristics (Table XXII), including homology to ICE family ofcysteine proteases. Several variants of 213P1F11, namely 213P1F11-v.2,-v.3 and -v.4, are novel proteins that maintain some homology to thepublished caspase 14 precursor (gi 6912286). For example, 213P1F11-v.2shows 100% identity to the human caspase 14 precursor (gi 6912286) overthe first 174 aa of the protein (FIG. 4D), while differing from thepublished caspase 14 precursor protein by 56 amino acids at itsC-terminus, thus resulting in 76% overall identity to caspase 14precursor. 213P1F11-v.2 also maintains homology to the mouse caspase 14,and shows 83% homology and 72% identity to that protein (gi 6753280)(FIG. 4F). The 213P1F11-v.3 variant protein show 100% identity to thehuman caspase 14 precursor (gi 6912286) over 134 amino acids, whilediffering from that protein by 12 aa at its C-terminus. Similarly,213P1F11-v.4 shows 97% identity with the human caspase 14 precursor over235 amino acids, while differing from the human caspase 14 precursor (gi6912286) by 86 aa at its N-terminus (FIG. 4G). 213P1F11-v.1 consists of242 amino acids, with calculated molecular weight of 28.0 kDa, and pI of5.4. 213P1F11-v.1 is an intercellular protein, located in the cytosolwith potential localization to the nucleus (Table XXII). Similarlocalization patterns are observed for 213P1F11 protein variants 1, 3,and 4 (Table XXII). Bioinformatic analysis indicates that 213P1F11-v.2may also localize to the mitochondria (Table XXII).

[0721] Caspases are a family of cyteine proteases that function aseffectors of apoptosis or programmed cell death (Salvesen G S, Dixit V,Cell. 1997, 91:443; Thomberry N, Lazebnik Y, Science. 281: 1312). Theseproteases cleave different cellular substrates in an aspartate-specificmanner. Cleavage may result in activation or inactivation of the cleavedcellular proteins, but not in protein degradation (Nunez et al,Oncogene. 1998, 17:3237; Stennicke H R, Salvesen G S, Cell Death Differ1999, 6:1054). Caspases traditionally exist as precursor proteins alsoknown as single polypeptide zymogens consisting of a pro-domain, and 2catalytic subunits, p20 and p1O and contain a conserved QACXG activesite (Stennicke H R, Salvesen G S, Cell Death Differ 1999, 6:1054; CohenM. Biochem J 1997, 326:1). Similar to other members of the caspasefamily, 213P1F11 contains two catalytic subunits, p20 and p10, inaddition to the conserved penta-peptide active site. In 213P1F11 v.1,p20 spans aa 16-139 and p10 spans aa 155-241, while the active site islocated at aa 129. Similarly, 213P1F11 v.4 carries both p20 and p10subunits, while 213P1F11 v.2 and v.3 contain the p20 subunit only,indicating that all 4 variants of 213P1F11 can function in a similarmanner. Caspases are activated by proteolytic cleavage of their internalaspartate by an upstream enzyme, often another caspase. However, unlikeother caspases with short pro-domains, caspase 14 is not reported toassociate with known caspases (Hu S et al, J. Biol. Chem. 1998,273:29648). Caspase 14 has been shown to be processed by caspase 8 andcaspase 10 as well as granzyme B, resulting in two catalytic subunits,p20 and p10 (Ahmad M et al, Cancer Res. 1998, 58:5201). These 2 cleavageproducts are detected in human epidermis and in vitro duringkeratinocyte differentiation (Eckhart L et al, J. Invest. Drmatol. 2000,115:1148). Overexpression of caspase 14 in breast carcinoma cells MCF7resulted in the apoptosis of these cells, suggesting that caspase 14participates in the process of programmed cell death (Hu S et al, J.Biol. Chem. 1998, 273:29648).

[0722] Our findings that 213P1F11 is highly expressed in several cancerswhile showing a restricted expression pattern in normal tissues suggeststhat the 213P1F11 gene plays an important role in various cancers,including cancers of the prostate, bladder and breast. Based on itssimilarity to caspase 14 213P1F11 has the ability to control tumorgrowth, apoptosis, survival, differentiation and progression.Accordingly, when 213P1F11 functions as a regulator of cell growth andapoptosis, or expression, 213P1F11 is used for therapeutic, diagnostic,prognostic or preventative purposes.

[0723] Our findings that 213P1F11 is highly expressed in several cancerswhile showing a restricted expression pattern in normal tissues suggeststhat the 213P1F11 gene plays an important role in various cancers,including cancers of the prostate, bladder and breast. Based on itssimilarity to caspase 14 213P1F11 has the ability to control tumorgrowth, apoptosis, survival, differentiation and progression.Accordingly, when 213P1F11 functions as a regulator of cell growth andapoptosis, or expression, 213P1F11 is used for therapeutic, diagnostic,prognostic or preventative purposes.

Example 45 Identification and Confirmation of Signal TransductionPathways

[0724] Many mammalian proteins have been reported to interact withsignaling molecules and to participate in regulating signaling pathways.(J. Neurochem. 2001; 76:217-223). Caspases participate in signaltransduction processes by getting recruited to signaling complexes andcleaving specific cellular substrates including other caspases andstructural proteins, ultimately resulting in morphologic changes thatrepresent the hallmark of apoptosis (Cohen G M. Biochem J. 1997, 326:1).Recent studies have demonstrated that caspases also cleave signalingmolecules, such as the guanine nucleotide exchange factor TIAM1, leadingto the inactivation of TIAMI and thereby the Rae cascade (Qi H et al,Cell Growth Differ. 2001, 12:603). Using iimmunoprecipitation andWestern blotting techniques, proteins are identified that associate with213P1F11 and mediate signaling events. Several pathways known to play arole in cancer biology can be regulated by 213P1F11, includingphospholipid pathways such as P13K, survival pathways such as AKT, NFkB,etc, adhesion and migration pathways, including FAK, Rho, Rac-1, etc, aswell as mitogenic/survival cascades such as ERK, p38, etc (Cell GrowthDiffer. 2000,11:279; J. Biol. Chem. 1999, 274:801; Oncogene. 2000,19:3003, J. Cell Biol. 1997, 138:913.). Bioinformatic analysis revealedthat 213P1F11 can become phosphorylated by serine/threonine as well astyrosine kinases. Thus, the phosphorylation of 213P1F11 is provided bythe present invention to lead to activation of the above listedpathways.

[0725] Using, e.g., Western blotting techniques the ability of 213P F11to regulate these pathways is confirmed. Cells expressing or lacking213P1F11 are either left untreated or stimulated with cytokines,hormones and anti-integrin antibodies. Cell lysates are analyzed usinganti-phospho-specific antibodies (Cell Signaling, Santa CruzBiotechnology) in order to detect phosphorylation and regulation of ERK,p38, AKT, P13K, PLC and other signaling molecules. When 213P1F11 plays arole in the regulation of signaling pathways, whether individually orcommunally, it is used as a target for diagnostic, prognostic,preventative and therapeutic purposes.

[0726] To confirm that 213P1F11 directly or indirectly activates knownsignal transduction pathways in cells, luciferase (luc) basedtranscriptional reporter assays are carried out in cells expressingindividual genes. These transcriptional reporters containconsensus-binding sites for known transcription factors that liedownstream of well-characterized signal transduction pathways. Thereporters and examples of these associated transcription factors, signaltransduction pathways, and activation stimuli are listed below.

[0727] NFkB-luc, NFkB/Rel; Ik-kinase/SAPK; growth/apoptosis/stress

[0728] SRE-luc, SRF/TCF/ELKI; MAPK/SAPK; growth/differentiation

[0729] AP-1-luc, FOS/JUN; MAPK/SAPK/PKC; growth/apoptosis/stress

[0730] ARE-luc, androgen receptor; steroids/MAPK;growth/differentiation/apoptosis

[0731] p53-luc, p53; SAPK; growth/differentiation/apoptosis

[0732] CRE-luc, CREB/ATF2; PKA/p38; growth/apoptosis/stress

[0733] Gene-mediated effects can be assayed in cells showing mRNAexpression. Luciferase reporter plasmids can be introduced bylipid-mediated transfection (TFX-50, Promega). Luciferase activity, anindicator of relative transcriptional activity, is measured byincubation of cell extracts with luciferin substrate and luminescence ofthe reaction is monitored in a luminometer.

[0734] Signaling pathways activated by 213P1F11 are mapped and used forthe identification and validation of therapeutic targets. When 213P1F11is involved in cell signaling, it is used as target for diagnostic,prognostic, preventative and therapeutic purposes.

Example 46 Involvement in Tumor Progression

[0735] Some apoptosis intermediates, such as DcRI, FLICE and TRAIL-R3,function as cellular inhibitors of apoptosis by acting as decoys andinterfering with normal function of the apoptotic machinery (Sheikh M Set al, Oncogene. 1999, 18:4153; Ashkenazi A, Dixit V M. Curr Opin CellBiol. 1999, 11:255). When 213P1F11 functions as a decoy, it cancontribute to the growth of cancer cells. The role of 213P1F11 in tumorgrowth is confirmed in a variety of primary and transfected cell linesincluding prostate, bladder and breast cell lines as well as NIH 3T3cells engineered to stably express 213P1F11. Parental cells lacking213P1F11 and cells expressing 213P1F11 are evaluated for cell growthusing a well-documented proliferation assay (Fraser S P, Grimes J A,Djamgoz M B. Prostate. 2000;44:61, Johnson D E, Ochieng J, Evans S L.Anticancer Drugs. 1996, 7:288).

[0736] To confirm the role of 213P1F11 in the transformation process,its effect in colony forming assays is investigated. Parental NIH3T3cells lacking 213P1F11 are compared to NHI-3T3 cells expressing213P1F11, using a soft agar assay under stringent and more permissiveconditions (Song Z. et al. Cancer Res. 2000, 60:6730).

[0737] To confirm the role of 213P1F11 in invasion and metastasis ofcancer cells, a well-established assay is used, e.g., a Transwell InsertSystem assay (Becton Dickinson) (Cancer Res. 1999, 59:6010). Controlcells. including prostate, colon, bladder and kidney cell lines lacking213P1F11 are compared to cells expressing 213P1F11. Cells are loadedwith the fluorescent dye, calcein, and plated in the top well of theTranswell insert coated with a basement membrane analog. Invasion isdetermined by fluorescence of cells in the lower chamber relative to thefluorescence of the entire cell population.

[0738] 213P1F11 can also play a role in cell cycle and apoptosis.Parental cells and cells expressing 213P1F11 are compared fordifferences in cell cycle regulation using a well-established BrdU assay(Abdel-Malek ZA. J Cell Physiol. 1988, 136:247). In short, cells aregrown under both optimal (full serum) and limiting (low serum)conditions are labeled with BrdU and stained with anti-BrdU Ab andpropidium iodide. Cells are analyzed for entry into the G1, S, and G2Mphases of the cell cycle. Alternatively, the effect of stress onapoptosis is evaluated in control parental cells and cells expressing213P1F11, including normal and tumor bladder cells. Engineered andparental cells are treated with various chemotherapeutic agents, such aspaclitaxel, gemcitabine, etc, and protein synthesis inhibitors, such ascycloheximide. Cells are stained with annexin V-FITC and cell death ismeasured by FACS analysis. The modulation of cell death by 213P1F11 canplay a critical role in regulating tumor progression and tumor load.

[0739] When 213P1F11 plays a role in cell growth, transformation,invasion or apoptosis, it is used as a target for diagnostic,prognostic, preventative and therapeutic purposes.

Example 47 Involvement in Angiogenesis

[0740] Angiogenesis or new capillary blood vessel formation is necessaryfor tumor growth (Hanahan D, Folkman J. Cell. 1996, 86:353; Folkman J.Endocrinology. 1998 139:441). Several assays have been developed tomeasure angiogenesis in vitro and in vivo, such as the tissue cultureassays, endothelial cell tube formation, and endothelial cellproliferation. Using these assays as well as in vitroneo-vascularization, the effect of 213P1F11 on angiogenesis isconfirmed. For example, endothelial cells engineered to express 213P1F11are evaluated using tube formation and proliferation assays. The effectof 213P1F11 is also confirmed in animal models in vivo. For example,cells either expressing or lacking 213P1F11 are implanted subcutaneouslyin immunocompromised mice. Endothelial cell migration and angiogenesisare evaluated 5-15 days later using immunohistochemistry techniques.When 213P1F11 affects angiogenesis, it is used as a target fordiagnostic, prognostic, preventative and therapeutic purposes

Example 48 Regulation of Transcription

[0741] The localization of 213P1F11 to the cytoplasm with potentialnuclear localization (Table XXII), support the present invention use of213P1F11 based on its role in the transcriptional regulation ofeukaryotic genes. Regulation of gene expression is confirmed, e.g., bystudying gene expression in cells expressing or lacking 213P1F11. Forthis purpose, two types of experiments are performed.

[0742] In the first set of experiments, RNA from parental and213P1F11-expressing cells are extracted and hybridized to commerciallyavailable gene arrays (Clontech) (Smid-Koopman E et al. Br J Cancer.2000. 83:246). Resting cells as well as cells treated with FBS orandrogen are compared. Differentially expressed genes are identified inaccordance with procedures known in the art. The differentiallyexpressed genes are then mapped to biological pathways (Chen K et al.,Thyroid. 2001. 11:41.).

[0743] In the second set of experiments, specific transcriptionalpathway activation is evaluated using commercially available(Stratagene) luciferase reporter constructs including: NFkB-luc,SRE-luc, ELK1-luc, ARE-luc, p53-luc, and CRE-luc. These transcriptionalreporters contain consensus binding sites for known transcriptionfactors that lie downstream of well-characterized signal transductionpathways, and represent a good tool to ascertain pathway activation andscreen for positive and negative modulators of pathway activation.

[0744] When 213P1F11 plays a role in gene regulation, it is used as atarget for diagnostic, prognostic, preventative and therapeuticpurposes.

Example 49 Subcellular Localization of 213P1F11

[0745] The cellular location of 213P1F11 can be assessed usingsubcellular fractionation techniques widely used in cellular biology(Storrie B, et al. Methods Enzymol. 1990;182:203-25). A variety of celllines, including prostate, bladder and breast cell lines as well as celllines engineered to express 213P1F11 are separated into nuclear,cytosolic and membrane fractions. Gene expression and location innuclei, heavy membranes (lysosomes, peroxisomes, and mitochondria),light membranes (plasma membrane and endoplasmic reticulum), and solubleprotein fractions are tested using Western blotting techniques.

[0746] Alternatively, 293T cells can be transfected with an expressionvector encoding individual genes, HIS-tagged (PcDNA 3.1 MYC/HIS,Invitrogen) and the subcellular localization of these genes isdetermined as described above. In short, the transfected cells can beharvested and subjected to a differential subcellular fractionationprotocol (Pemberton, P. A. et al, 1997, J of Histochemistry andCytochemistry, 45:1697-1706.). Location of the HIS-tagged genes isfollowed by Western blotting.

[0747] Using 213P1F11 antibodies, it is possible to demonstrate cellularlocalization by irumunofluorescence and immunohistochemistry. Forexample, cells expressing or lacking 213P1F11 are adhered to amicroscope slide and stained with anti-213P1F11 specific Ab. Cells areincubated with an FITC-coupled secondary anti-species Ab, and analyzedby fluorescent microscopy.

[0748] When 213P1F11 is localized to specific cell compartments, it isused as a target for diagnostic, preventative and therapeutic purposes.

Example 50 213P1F11 Proteolytic Activity

[0749] The similarity of 213P1F11 to casapase cysteine proteasessupports the use of 213P1F11 as a protease. Protease activity can beconfirmed using on in vitro protease assay coupled to detection ofprotein fragments by western blotting (Hu S et al, above; Slee E et al,J. Biol. Chem. 2001, 276:7320). In one embodiment, recombinant 213P1F11protein is incubated with apoptotic substrates, including other caspasesknown to associate with caspase 14, namely caspase 2 and caspase 4, aswell as recombinant RIP and poly(ADP-ribose) polymerase (i.e. PARP)(Slee E et al, J. Biol. Chem. 2001, 276:7320; Hayakawa et al, Apoptosis.2002, 7:107). Proteins are separated by SDS-Page and analyzed by westernblotting with substrate specific antibodies. In another embodiment,213P1F11 activity is compared in control cells lacking 213P1F11 andcells expressing 213P1F11. Cell lysates from control and 213P1F11expressing cells are incubated in the presence of the recombinantsubstrates listed above. Whole proteins are analyzed by western blottingwith antibodies directed to the apoptotic substrates.

[0750] When 213P1F11 functions as a protease, it is used as a target fordiagnostic, preventative and therapeutic purposes Throughout thisapplication, various website data content, publications, patentapplications and patents are referenced. (Websites are referenced bytheir Uniform Resource Locator, or URL, addresses on the World WideWeb.) The disclosures of each of these references are herebyincorporated by reference herein in their entireties.

[0751] The present invention is not to be limited in scope by theembodiments disclosed herein, which are intended as single illustrationsof individual aspects of the invention, and any that are functionallyequivalent are within the scope of the invention. Various modificationsto the models and methods of the invention, in addition to thosedescribed herein, will become apparent to those skilled in the art fromthe foregoing description and teachings, and are similarly intended tofall within the scope of the invention. Such modifications or otherembodiments can be practiced without departing from the true scope andspirit of the invention. TABLE I Tissues that Express 213P1F11 WhenMalignant Bladder Prostate Breast

[0752] TABLE II Amino Acid Abbreviations SINGLE LETTER THREE LETTER FULLNAME F Phe phenylalanine L Leu leucine S Ser serine Y Tyr tyrosine C Cyscysteine W Trp tryptophan P Pro proline H His histidine Q Gln glutamineR Arg arginine I Ile isoleucine M Met methiomne T Thr threonine N Asnasparagine K Lys lysine V Val valine A Ala alanine D Asp aspartic acid EGlu glutamic acid G Gly glycine

[0753] TABLE III AMINO ACID SUBSTITUTION MATRIX Adapted from the GCGSoftware 9.0 BLOSUM62 amino acid substitution matrix (block substitutionmatrix). The higher the value, the more likely a substitution is foundin related, natural proteins. (See URLwww.ikp.unibe.ch/manual/blosum62.html) A C D E F G H I K L M N P Q R S TV W Y . 4 0 −2 −1 −2 0 −2 −1 −1 −1 −1 −2 −1 −1 −1 1 0 0 −3 −2 A 9 −3 −4−2 −3 −3 −1 −3 −1 −1 −3 −3 −3 −3 −1 −1 −1 −2 −2 C 6 2 −3 −1 −1 −3 −1 −4−3 1 −1 0 −2 0 −1 −3 −4 −3 D 5 −3 −2 0 −3 1 −3 −2 0 −1 2 0 0 −1 −2 −3 −2E 6 −3 −1 0 −3 0 0 −3 −4 −3 −3 −2 −2 −1 1 3 F 6 −2 −4 −2 −4 −3 0 −2 −2−2 0 −2 −3 −2 −3 G 8 −3 −1 −3 −2 1 −2 0 0 −1 −2 −3 −2 2 H 4 −3 2 1 −3 −3−3 −3 −2 −1 3 −3 −1 I 5 −2 −1 0 −1 1 2 0 −1 −2 −3 −2 K 4 2 −3 −3 −2 −2−2 −1 1 −2 −1 L 5 −2 −2 0 −1 −1 −1 1 −1 −1 M 6 −2 0 0 1 0 −3 −4 −2 N 7−1 −2 −1 −1 −2 −4 −3 P 5 1 0 −1 −2 −2 −1 Q 5 −1 −1 −3 −3 −2 R 4 1 −2 −3−2 S 5 0 −2 −2 T 4 −3 −1 V 11 2 W 7 Y

[0754] TABLE IV HLA Class I/II Motifs/Supermotifs TABLE IV (A): HLAClass I Supermotifs/Motifs POSITION POSITION POSITION 2 (Primary Anchor)3 (Primary Anchor) C Terminus (Primary Anchor) SUPERMOTIFS A1 TILVMS FWYA2 LIVMATQ IVMATL A3 VSMATLI RK A24 YFWIVLMT FIYWLM B7 P VILFMWYA B27RHK FYLWMIVA B44 ED FWYLIMVA B58 ATS FWVLIVMA B62 QLIVMP FWYMIVLA MOTIFSA1 TSM Y A1 DEAS Y A2.1 LMVQIAT VLIMAT A3 LMVISATFCGD KYRHFA A11VTMLISAGNCDF KRYH A24 YFWM FLIW A*3101 MVTALIS RK A*3301 MVALFIST RKA*6801 AVTMSLI RK B*0702 P LMFWYAIV B*3501 P LMFWYIVA B51 P LIVFWYAMB*5301 P IMFWYALV B*5401 P ATIVLMFWY TABLE IV (B): HLA Class IISupermotif 1 6 9 W, F, Y, V, .I, L A, V, I, L, P, C, S, T A, V, I, L, C,S, T, M, Y TABLE IV (C): HLA Class II Motifs MOTIFS 1° anchor 1 2 3 4 51° anchor 6 7 8 9 DR4 preferred FMYLIVW M T I VSTCPALIM MH MHdeleterious W R WDE DR1 preferred MFLIVWY PAMQ VMATSPLIC M AVMdeleterious C CH FD CWD GDE D DR7 preferred MFLIVWY M W A IVMSACTPL M IVdeleterious C G GRD N G DR3 MOTIFS 1° anchor 1 2 3 1° anchor 4 5 1°anchor 6 motif a preferred LIVMFY D motif b preferred LIVMFAY DNQEST KRHDR MFLIVWY VMSTACPLI Supermotif TABLE IV (D): HLA Class I SupermotifsPOSITION: SUPERMOTIFS 1 2 3 4 5 6 7 8 C-terminus A1  1° Anchor 1° AnchorTILVMS FWY A2  1° Anchor 1° Anchor LIVMATQ LIVMAT A3  preferred1° Anchor YFW (4/5) YFW (3/5) YFW (4/5) P (4/5) 1° Anchor VSMATLI RKdelete- DE (3/5); DE (4/5) rious P (5/5) A24 1° Anchor 1° AnchorYFWIVLMT FIYWLM B7  preferred FWY (5/5) 1° Anchor FWY (4/5) FWY (3/5)1° Anchor LIVM (3/5) P VILFMWYA delete- DE (3/5); DE (3/5) G (4/5) QN(4/5) DE (4/5) rious P (5/5); G (4/5); A (3/5); QN (3/5) B27 1° Anchor1° Anchor RHK FYLWMIVA B44 1° Anchor 1° Anchor ED FWYLIMVA B58 1° Anchor1° Anchor ATS FWYLIVMA B62 1° Anchor 1° Anchor QLIVMP FWYMIVLA TABLE IV(E): HLA Class I Motifs POSITION: C- 1 2 3 4 5 6 7 8 9 terminus orC-terminus A1 preferred GFY 1° Anchor DEA YFW P DEQN YFW 1° Anchor 9-merW STM Y deleterious DE RHKLIVMP A G A A1 preferred GRHK ASTCLIVM1° Anchor GSTC ASTC LIVM DE 1° Anchor 9-mer DEAS Y deleterious A RHKDEPYDE PQN RHK PG GP FW A1 preferred YFW 1° Anchor DEAQN A YFWQN PASTC GDE P1° Anchor 10-mer STM Y deleterious GP RHKGLIVM DE RHK QNA RHKYFW RHK AA1 preferred YFW STCLIVM 1° Anchor A YFW PG G YFW 1° Anchor 10-mer DEASY deleterious RHK RHKDEPY P G PRHK QN FW A2.1 preferred YFW 1° AnchorYFW STC YFW A P 1° Anchor 9-mer {overscore (LMIVQAT)} VLIMAT deleteriousDEP DERKH RKH DERKH POSITION: C- 1 2 3 4 5 6 7 8 9 Terminus A2.1preferred AYFW 1° Anchor LVIM G G FYWL 1° Anchor 10-mer LMIVQA VIMVLIMAT T deleterious DEP DE RKHA P RKH DERKH RKH A3 preferred RHK1° Anchor YFW PRHKYFW A YFW P 1° Anchor LMVISA KYRHFA TFCGD deleteriousDEP DE A11 preferred A 1° Anchor YFW YFW A YFW YFW P 1° Anchor VTLMISKRYH AGNCDF deleterious DEP A G A24 preferred YFWRHK 1° Anchor STC YFWYFW 1° Anchor 9-mer YFWM FLIW deleterious DEG DE G QNP DERH G AQN K A24preferred 1° Anchor P YFWP P 1° Anchor 10-mer YFWM FLIW deleterious GDEQN RHK DE A QN DEA A3101 preferred RHK 1° Anchor YFW P YFW YFW AP1° Anchor {overscore (MVTALIS)} RK deleterious DEP DE ADE DE DE DE A3301preferred 1° Anchor YFW AYFW 1° Anchor MVALFI RK ST deleterious GP DEPOSITION: C- 1 2 3 4 5 6 7 8 9 Terminus A6801 preferred YFWSTC 1° AnchorYFWLIV YFW P 1° Anchor {overscore (AVTMSLI)} M RK deleterious GP DEG RHKA B0702 preferred RHKFW 1° Anchor RHK RHK RHK RHK PA  1° Anchor Y P{overscore (LMFWYAIV)} deleterious DEQNP DEP DE DE GDE QN DE B3501preferred FWYLIV 1° Anchor FWY FWY 1° Anchor M P {overscore (LMFWYIV)} Adeleterious AGP G G B51 preferred LIVMFW 1° Anchor FWY STC FWY G FWY  1°Anchor Y P {overscore (LIVFWYAM)} deleterious AGPDER DE G DEQN GDE HKSTCB5301 preferred LIVMFW 1° Anchor FWY STC FWY LIVMFWY FWY 1° Anchor Y P{overscore (IMFWYAL)} V deleterious AGPQN G RHKQN DE B5401 preferred FWY1° Anchor FWYL LIVM ALIVM FWYAP 1° Anchor P IVM {overscore (ATIVLMF)} WYdeleterious GPQNDE GDES RHKDE DE QNDGE DE TC

[0755] TABLE V Pos 123456789 Score SeqID v.1-A1-9 mers: 213P1F11 96KGEDGEMVK 22.500 215 EAELVQEGK 18.000 171 TVEGYIAYR 18.000 191 LVDVFTKRK10.000 170 STVEGYIAY 6.250 35 DLDALEHMF 5.000 75 REDPVSCAF 2.500 53KRDPTAEQF 2.500 162 YTDALHVYS 2.500 189 QTLVDVFTK 2.500 228 NPEIQSTLR2.250 206 LTEVTRRMA 2.250 6 SLEEEKYDM 1.800 145 GDEIVMVIK 1.800 154DSPQTIPTY 1.500 31 GSEEDLDAL 1.350 99 DGEMVKLEN 1.125 104 KLENLFEAL0.900 57 TAEQFQEEL 0.900 202 ILELLTEVT 0.900 38 ALEHMFRQL 0.900 232QSTLRKRLY 0.750 144 GGDEIVMVI 0.625 167 HVYSTVEGY 0.500 71 AIDSREDPV0.500 19 LALILCVTK 0.400 218 LVQEGKARK 0.400 136 QRDPGETVG 0.250 179RHDQKGSCF 0.250 157 QTIPTYTDA 0.250 226 KTNPEIQST 0.250 62 QEELEKFQQ0.225 175 YIAYRHDQK 0.200 125 KVYITQACR 0.200 107 ILFEALNNK 0.200 213MAEAELVQE 0.180 59 EQFQEELEK 0.150 219 VQEGKARKT 0.135 61 FQEELEKFQ0.135 33 EEDLDALEH 0.125 217 ELVQEGKAR 0.100 204 ELLTEVTRR 0.100 187FIQTLVDVF 0.100 21 LILCVTKAR 0.100 190 TLVDVFTKR 0.100 83 FVVLMAHGR0.100 230 EIQSTLRKR 0.100 64 ELEKFQQAI 0.090 1 MSNPRSLEE 0.075 115KNCQALRAK 0.050 97 GEDGEMVKL 0.050 86 LMAHGREGF 0.050 142 TVGGDEIVM0.050 37 DALEHMFRQ 0.050 80 SCAFVVLMA 0.050 119 ALRAKPKVY 0.050 11KYDMSGARL 0.050 81 CAFVVLMAH 0.050 108 LFEALNNKN 0.045 133 RGEQRDPGE0.045 74 SREDPVSCA 0.045 7 LEEEKYDMS 0.045 28 AREGSEEDL 0.045 169YSTVEGYIA 0.030 117 CQALRAKPK 0.030 79 VSCAFVVLM 0.030 14 MSGARLALI0.030 36 LDALEHMFR 0.025 46 LRFESTMKR 0.025 141 ETVGGDEIV 0.025 212RMAEAELVQ 0.025 40 EHMFRQLRF 0.025 13 DMSGARLAL 0.025 153 KDSPQTIPT0.025 161 TYTDALHVY 0.025 8 EEEKYDMSG 0.022 45 QLRFESTMK 0.020 121PAKPKVYII 0.020 49 ESTMKRDPT 0.015 129 IQACRGEQR 0.015 184 GSCFIQTLV0.015 199 KGHILELLT 0.013 233 STLRKRLYL 0.013 30 EGSEEDLDA 0.013 77DPVSCAFVV 0.013 106 ENLFEALNN 0.013 160 PTYTDALHV 0.013 128 IIQACRGEQ0.010 20 ALILCVTKA 0.010 158 TIPTYTDAL 0.010 18 RLALILCVT 0.010 164DALHVYSTV 0.010 111 ALNNKNCQA 0.010 193 DVFTKRKGH 0.010 85 VLMAHGREG0.010 205 LLTEVTRRM 0.010 203 LELLTEVTR 0.010 147 EIVMVIKDS 0.010 110EALNNKNCQ 0.010 23 LCVTKAREG 0.010 v.2-A1-9 mers: 213P1F11 33 DTSPTDMIR12.500 12 FQDPLYLPS 3.750 5 TVEGPTPFQ 1.800 34 TSPTDMIRK 1.500 9PTPFQDPLY 0.250 4 STVEGPTPF 0.250 21 EAPPNPPLW 0.200 36 PTDMIRKAH 0.12546 LSRPWWMCS 0.075 31 SQDTSPTDM 0.075 8 GPTPFQDPL 0.025 17 YLPSEAPPN0.020 19 PSEAPPNPP 0.014 22 APPNPPLWN 0.013 10 TPFQDPLYL 0.013 42KAHALSRPW 0.010 20 SEAPPNPPL 0.010 44 HALSRPWWM 0.010 50 WWMCSRRGK 0.01047 SRPWWMCSR 0.005 3 YSTVEGPTP 0.003 30 NSQDTSPTD 0.003 40 IRKAHALSR0.003 24 PNPPLWNSQ 0.003 56 RGKDISWNF 0.003 23 PPNPPLWNS 0.003 14DPLYLPSEA 0.003 35 SPTDMIRKA 0.003 6 VEGPTPFQD 0.003 48 RPWWMCSRR 0.00329 WNSQDTSPT 0.003 37 TDMIRKAHA 0.001 52 MCSRRGKDI 0.001 45 ALSRPWWMC0.001 16 LYLPSEAPP 0.001 1 HVYSTVEGP 0.001 43 AHALSRPWW 0.001 51WMCSRRGKD 0.001 32 QDTSPTDMI 0.001 38 DMIRKAHAL 0.001 18 LPSEAPPNP 0.0012 VYSTVEGPT 0.001 54 SRRGKDISW 0.000 25 NPPLWNSQD 0.000 26 PPLWNSQDT0.000 7 EGPTPFQDP 0.000 39 MIRKAHALS 0.000 53 CSRRGKDIS 0.000 15PLYLPSEAP 0.000 13 QDPLYLPSE 0.000 27 PLWNSQDTS 0.000 41 RKAHALSRP 0.00028 LWNSQDTSP 0.000 55 RRGKDTSWN 0.000 11 PFQDPLYLP 0.000 49 PWWMCSRRG0.000 v.3-A1-9 mers: 213P1F11 9 ATLPSPFPY 62.500 11 LPSPFPYLS 0.050 7RGATLPSPF 0.025 10 TLPSPFPYL 0.020 1 YIIQACRGA 0.010 2 IIQACRGAT 0.01012 PSPFPYLSL 0.008 5 ACRGATLPS 0.005 3 IQACRGATL 0.003 8 GATLPSPFP 0.0024 QACRGATLP 0.000 6 CRGATLPSP 0.000 v.4-A1-9 mers: 213P1F11 85 ASEEEKYDM2.700 25 NGECGQTFR 2.250 35 KEEQGRAFR 0.900 83 TSASEEEKY 0.750 9KSLSVQPEK 0.600 82 ETSASEEEK 0.500 34 LKEEQGRAF 0.450 71 GRDLSISFR 0.25014 QPEKRTGLR 0.225 27 ECGQTFRLK 0.200 80 NSETSASEE 0.135 58 TQEVFGGGV0.135 4 CQEYDKSLS 0.135 52 VNDPRETQE 0.125 66 VGDIVGRDL 0.125 10SLSVQPEKR 0.100 12 SVQPEKRTG 0.100 45 SSVHQKLVN 0.075 68 DIVGRDLSI 0.05064 GGVGDIVGR 0.050 86 SEEEKYDMS 0.045 22 RDENGECGQ 0.045 57 ETQEVFGGG0.025 24 ENGECGQTF 0.025 18 RTGLRDENG 0.025 21 LRDENGECG 0.025 44GSSVHQKLV 0.015 11 LSVQPEKRT 0.015 70 VGRDLSISF 0.013 63 GGGVGDIVG 0.01351 LVNDPRETQ 0.010 3 KCQEYDKSL 0.010 73 DLSISFRNS 0.010 1 MGKCQEYDK0.010 50 KLVNDPRET 0.010 75 SISFRNSET 0.010 42 FRGSSVHQK 0.010 55PRETQEVFG 0.009 54 DPRETQEVF 0.003 5 QEYDKSLSV 0.003 56 RETQEVFGG 0.00372 RDLSISFRN 0.003 6 EYDKSLSVQ 0.003 62 FGGGVGDIV 0.003 30 QTFRLKEEQ0.003 36 EEQGRAFRG 0.003 26 GECGQTFRL 0.003 43 RGSSVHQKL 0.003 46SVHQKLVND 0.002 60 EVFGGGVGD 0.002 76 ISFRNSETS 0.002 74 LSISFRNSE 0.00248 HQKLVNDPR 0.002 13 VQPEKRTGL 0.002 28 CGQTFRLKE 0.001 84 SASEEEKYD0.001 69 IVGRDLSIS 0.001 20 GLRDENGEC 0.001 33 RLKEEQGPA 0.001 40RAFRGSSVH 0.001 65 GVGDIVGRD 0.001 32 FRLKEEQGR 0.001 59 QEVFGGGVG 0.00161 VFGGGVGDT 0.001 78 FRNSETSAS 0.001 67 GDIVGRDLS 0.001 23 DENGECGQT0.001 79 RNSETSASE 0.001 2 GKCQEYDKS 0.001 39 GPAFRGSSV 0.001 17KRTGLRDEN 0.001 38 QGRAFRGSS 0.000 37 EQGRAFRGS 0.000 29 GQTFRLKEE 0.00041 AFRGSSVHQ 0.000 49 QKLVNDPRE 0.000 8 DKSLSVQPE 0.000 81 SETSASEEE0.000 31 TFRLKEEQG 0.000 77 SFRNSETSA 0.000 53 NDPRETQEV 0.000 19TGLRDENGE 0.000 7 YDKSLSVQP 0.000 47 VHQKLVNDP 0.000 16 EKRTGLRDE 0.00015 PEKRTGLRD 0.000 v.5-A1-9 mers: 213P1F11 4 LALILRVTK 0.400 1 GARLALILR0.050 5 ALILRVTKA 0.010 6 LILRVTKAR 0.010 3 RLALILRVT 0.010 2 ARLALILRV0.003 9 RVTKAREGS 0.001 8 LRVTKAREG 0.001 7 ILRVTKARE 0.000 v.6-A1-9mers: 213P1F11 1 KLENLFEAM 0.900 4 NLFEANNNK 0.200 5 LFEAMNNKN 0.045 3ENLFEAMNN 0.013 7 EAMNNKNCQ 0.010 8 AMNNKNCQA 0.005 2 LENLFEAMN 0.001 6FEAMNNKNC 0.001 9 MNNKNCQAL 0.000

[0756] TABLE VI Pos 1234567890 Score SeqID v.1-A1-10 mers: 213P1F11 35DLDALEHMFR 25.000 228 NPEIQSTLRK 22.500 202 ILELLTEVTR 18.000 38ALEHMFRQLR 9.000 144 GGDEIVMVIK 5.000 169 YSTVEGYIAY 3.750 162YTDALHVYST 2.500 104 KLENLFEALN 1.800 171 TVEGYIAYRH 1.800 206LTEVTRRMAE 1.125 87 MAHGREGFLK 1.000 71 AIDSREDPVS 1.000 215 EAELVQEGKA0.900 213 MAEAELVQEG 0.900 6 SLEEEKYDMS 0.900 61 FQEELEKFQQ 0.675 75REDPVSCAFV 0.500 136 QRDPGETVGG 0.500 153 KDSPQTIPTY 0.500 191LVDVFTKRKG 0.500 170 STVEGYIAYR 0.500 96 KGEDGEMVKL 0.450 74 SREDPVSCAF0.450 18 RLALILCVTK 0.400 217 ELVQEGKARK 0.400 31 GSEEDLDALE 0.270 189QTLVDVFTKR 0.250 226 KTNPEIQSTL 0.250 53 KRDPTAEQFQ 0.250 157 QTIPTYTDAL0.250 133 RGEQRDPGET 0.225 7 LEEEKYDMSG 0.225 32 SEEDLDALEH 0.225 99DGEMVKLENL 0.225 116 NCQALRAKPK 0.200 190 TLVDVFTKRK 0.200 188IQTLVDVFTK 0.150 219 VQEGKARKTN 0.135 141 ETVGGDEIVM 0.125 160PTYTDALHVY 0.125 152 IKDSPQTIPT 0.125 20 ALILCVTKAP 0.100 128 IIQACRGEQR0.100 85 VLMAHGREGF 0.100 57 TAEQFQEELE 0.090 232 QSTLRKRLYL 0.075 14MSGARLALIL 0.075 231 IQSTLRKRLY 0.075 79 VSCAFVVLMA 0.075 121 RAKPKVYIIQ0.050 118 QALRAKPKVY 0.050 80 SCAFVVLMAH 0.050 106 ENLFEALNNK 0.050 95LKGEDOEMVK 0.050 58 AEQFQEELEK 0.050 45 QLRFESTMKR 0.050 108 LFEALNNKMC0.045 62 QEELEKFQQA 0.045 5 RSLEEEKYDM 0.030 49 ESTMKRDPTA 0.030 179RHDQKGSCFI 0.025 11 KYDMSGARLA 0.025 39 LEHMFRQLRF 0.025 166 LHVYSTVEGY0.025 33 EEDLDALEHM 0.025 227 TNPEIQSTLR 0.025 139 PGETVGGDEI 0.022 145GDEIVMVIKD 0.022 142 TVGGDEIVMV 0.020 165 ALHVYSTVEG 0.020 185SCFIQTLVDV 0.020 81 CAFVVLMAHG 0.020 187 FIQTLVDVFT 0.020 158 TIPTYTDALH0.020 64 ELEKFQQAID 0.018 59 EQFQEELEKF 0.015 1 MSNPRSLEEE 0.015 154DSPQTIPTYT 0.015 159 IPTYTDALHV 0.013 3 NPRSLEEEKY 0.013 143 VGGDEIVMVI0.013 111 ALNNKNCQAL 0.010 19 LALILCVTKA 0.010 70 QAIDSREDPV 0.010 167HVYSTVEGYI 0.010 125 KVYIIQACRG 0.010 114 NKNCQALRAK 0.010 22 ILCVTKAREG0.010 149 VMVIKDSPQT 0.010 204 ELLTEVTRRM 0.010 110 EALNNKNCQA 0.010 13DMSGARLALI 0.010 23 LCVTKAREGS 0.010 175 YIAYRHDQKG 0.010 148 IVMVIKDSPQ0.010 84 VVLMAHGREG 0.010 230 EIQSTLRKRL 0.010 214 AEAELVQEGK 0.010 201HILELLTEVT 0.010 193 DVFTKRKGHI 0.010 v.2-A1-10 mers: 213P1F11 34DTSPTDMIRK 25.000 9 GPTPFQDPLY 2.500 22 EAPPNPPLWM 0.500 6 TVEGPTPFQD0.450 20 PSEAPPNPPL 0.270 37 PTDMIRKAHA 0.250 47 LSRPWWMCSR 0.150 4YSTVEGPTPF 0.150 13 FQDPLYLPSE 0.150 32 SQDTSPTDMI 0.075 5 STVEGPTPFQ0.050 33 QDTSPTDMIR 0.025 43 KAHALSRPWW 0.020 31 NSQDTSPTDM 0.015 35TSPTDMIRKA 0.015 10 PTPFQDPLYL 0.013 45 HALSRPWWMC 0.010 21 SEAPPNPPLW0.010 17 LYLPSEAPPN 0.010 2 HVYSTVEGPT 0.010 40 MIRKAHALSR 0.005 52WMCSRRGKDI 0.005 46 ALSRPWWMCS 0.005 48 SRPWWMCSRR 0.005 8 EGPTPFQDPL0.003 26 NPPLWNSQDT 0.003 24 PPNPPLWNSQ 0.003 36 SPTDMIRKAH 0.003 23APPNPPLWNS 0.003 18 YLPSEAPPNP 0.002 39 DMIRKAHALS 0.001 53 MCSRRGKDIS0.001 54 CSRRGKDISW 0.001 56 RRGKDISWNF 0.001 42 RKAHALSRPW 0.001 44AHALSRPWWM 0.001 14 QDPLYLPSEA 0.001 11 TPFQDPLYLP 0.001 38 TDMIRKAHAL0.001 29 LWNSQDTSPT 0.001 7 VEGPTPFQDP 0.001 30 WNSQDTSPTD 0.001 12PFQDPLYLPS 0.000 27 PPLWNSQDTS 0.000 19 LPSEAPPNPP 0.000 15 DPLYLPSEAP0.000 25 PNPPLWNSQD 0.000 49 RPWWMCSRRG 0.000 16 PLYLPSEAPP 0.000 50PWWMCSRRGK 0.000 3 VYSTVEGPTP 0.000 55 SRRGKDISWN 0.000 1 LHVYSTVEGP0.000 51 WWMCSRRGKD 0.000 28 PLWNSQDTSP 0.000 41 IRKAHALSRP 0.000v.3-A1-10 mers: 213P1F11 9 CATLPSPFPY 2.500 10 ATLPSPFPYL 0.500 12LPSPFPYLSL 0.125 11 TLPSPFPYLS 0.020 3 IIQACRGATL 0.020 2 YIIQACRGAT0.010 7 CRGATLPSPF 0.005 5 QACRGATLPS 0.005 1 VYIIQACRGA 0.001 8RGATLPSPFP 0.001 6 ACRGATLPSP 0.000 4 IQACRGATLP 0.000 v.4-A1-10 mers:213P1F11 85 ASEEEKYDMS 1.350 82 ETSASEEEKY 1.250 52 VNDPRETQEV 1.250 25NGECGQTFRL 1.125 34 LKEEQGRAFR 0.900 4 CQEYDKSLSV 0.675 35 KEEQGRAFRG0.225 86 SEEEKYDMSG 0.225 9 KSLSVQPEKR 0.150 80 NSETSASEEE 0.135 58TQEVFGGGVG 0.135 66 VGDIVGRDLS 0.125 71 GRDLSISFRN 0.125 12 SVQPEKRTGL0.100 44 GSSVHQKLVN 0.075 63 GGGVGDIVGR 0.050 69 IVGRDLSISF 0.050 22RDENGECGQT 0.045 57 ETQEVFGGGV 0.025 24 ENGECGQTFR 0.025 21 LRDENGECGQ0.025 55 PRETQEVFGG 0.023 84 SASEEEKYDM 0.020 8 DKSLSVQPEK 0.020 11LSVQPEKRTG 0.015 13 VQPEKRTGLR 0.015 74 LSISFRNSET 0.015 62 FGGGVGDIVG0.013 14 QPEKRTGLRD 0.011 10 SLSVQPEKRT 0.010 60 EVFGGGVGDI 0.010 75SISFRNSETS 0.010 65 GVGDIVGRDL 0.010 3 KCQEYDKSLS 0.010 68 DIVGRDLSIS0.010 81 SETSASEEEK 0.010 26 GECGQTFRLK 0.010 33 RLKEEQGRAF 0.010 50KLVNDPRETQ 0.010 23 DENGECGQTF 0.005 27 ECGQTFRLKE 0.005 45 SSVHQKLVND0.003 67 GDIVGRDLSI 0.003 70 VGRDLSISFR 0.003 30 QTFRLKEEQG 0.003 18RTGLRDENGE 0.003 43 RGSSVHQKLV 0.003 40 RAFRCSSVHQ 0.002 83 TSASEEEKYD0.002 76 TSFRNSETSA 0.002 29 GQTFRLKEEQ 0.002 41 AFRGSSVHQK 0.001 20GLRDENGECG 0.001 73 DLSISFRNSE 0.001 51 LVNDPRETQE 0.001 46 SVHQKLVNDP0.001 47 VHQKLVNDPR 0.001 31 TFRLKEEQGR 0.001 53 NDPRETQEVF 0.001 49QKLVNDPRET 0.001 2 GKCQEYDKSL 0.001 56 RETQEVFGGG 0.001 6 EYDKSLSVQP0.001 54 DPRETQEVFG 0.001 39 GRAFRGSSVH 0.001 42 FRGSSVHQKL 0.001 61VFGGGVGDIV 0.001 5 QEYDKSLSVQ 0.001 72 RDLSISFRNS 0.001 17 KRTGLRDENG0.001 36 EEQGRAFRGS 0.001 79 RNSETSASEE 0.000 1 MGKCQEYDKS 0.000 38QGRAFRGSSV 0.000 19 TGLRDENGEC 0.000 64 GGVGDIVGRD 0.000 28 CGQTFRLKEE0.000 37 EQGRAFRGSS 0.000 78 FRNSETSASE 0.000 59 QEVFGGGVGD 0.000 77SFRNSETSAS 0.000 16 EKRTGLRDEN 0.000 32 FRLKEEQGRA 0.000 48 HQKLVNDPRE0.000 7 YDKSLSVQPE 0.000 15 PEKRTGLRDE 0.000 v.5-A1-10 mers: 213P1F11 4RLALILRVTK 0.400 6 ALILRVTKAR 0.100 1 SGARLALILR 0.013 5 LALILRVTKA0.010 2 GARLALILRV 0.005 8 ILRVTKAREG 0.001 9 LRVTKAREGS 0.001 3ARLALILRVT 0.001 7 LILRVTKARE 0.000 10 RVTKAREGSE 0.000 v.6-A1-10 mers:213P1F11 2 KLENLFEANN 1.800 4 ENLFEANNNK 0.050 6 LFEAMNNKNC 0.045 8EAMNNKNCQA 0.010 5 HLFEANNNKN 0.010 10 MNNKNCQALR 0.005 9 AMNNKNCQAL0.005 3 LENLFEAMNN 0.003 7 FEANNNKNCQ 0.001 1 VKLENLFEAM 0.001

[0757] TABLE VII Pos 123456789 Score SeqID v.1-A2-9 mers: 213P1F11 20ALILCVTKA 11.426 201 HILELLTEV 11.345 143 VGGDEIVMV 7.278 44 RQLRFESTM7.082 188 IQTLVDVFT 7.064 18 RLALILCVT 7.027 205 LLTEVTRRM 6.925 233STLRKRLYL 6.038 111 ALNNKNCQA 4.968 104 KLENLFEAL 4.455 183 KGSCFIQTL4.266 231 IQSTLRKRL 3.682 118 QALRAKPKV 3.574 103 VKLENLFEA 2.374 71AIDSREDPV 1.874 100 GEMVKLENL 1.732 158 TIPTYTDAL 1.439 6 SLEEEKYDM1.304 13 DMSGARLAL 1.157 150 MVIKDSPQT 1.108 226 KTNPEIQST 0.833 227TNPEIQSTL 0.572 107 NLFEALNNK 0.520 38 ALEHMFRQL 0.520 79 VSCAFVVLM0.482 184 GSCFIQTLV 0.454 109 FEALNNKNC 0.444 164 DALHVYSTV 0.402 97GEDGEMVKL 0.382 87 MAHGREGFL 0.361 151 VIKDSPQTI 0.350 95 LKGEDGEMV0.330 155 SPQTIPTYT 0.268 14 MSGARLALI 0.266 50 STMKRDPTA 0.255 112LNNKNCQAL 0.237 63 EELEKFQQA 0.209 64 ELEKFQQAI 0.190 142 TVGGDEIVM0.178 199 KGHILELLT 0.170 202 ILELLTEVT 0.163 190 TLVDVFTKR 0.116 186CFIQTLVDV 0.111 144 GGDEIVMVT 0.105 94 FLKGEDGEM 0.104 157 QTIPTYTDA0.104 140 GETVGGDEI 0.099 85 VLMAHGREG 0.094 17 ARLALILCV 0.082 77DPVSCAFVV 0.081 135 EQRDPGETV 0.081 208 EVTRRMAEA 0.075 80 SCAFVVLMA0.075 160 PTYTDALHV 0.068 169 YSTVEGYIA 0.061 15 SGARLALIL 0.057 216AELVQEGKA 0.046 86 LMAHGREGF 0.045 31 GSEEDLDAL 0.041 76 EDPVSCAFV 0.040223 KARKTNPEI 0.039 153 KDSPQTIPT 0.036 57 TAEQFQEEL 0.035 198 RKGHILELL0.033 78 PVSCAFVVL 0.032 22 ILCVTKARE 0.025 163 TDALHVYST 0.024 12YDMSGARLA 0.023 187 FIQTLVDVF 0.022 182 QKGSCFIQT 0.020 195 FTKRKGHIL0.020 134 GEQRDPGET 0.019 149 VMVIKDSPQ 0.018 212 RMAEAELVQ 0.018 211RRMAEAELV 0.018 219 VQEGKARKT 0.016 125 KVYIIQACR 0.015 141 ETVGGDEIV0.015 214 AEAELVQEG 0.014 120 LRAKPKVYI 0.014 21 LILCVTKAR 0.013 16GARLALILC 0.012 162 YTDALHVYS 0.010 189 QTLVDVFTK 0.010 61 FQEELEKFQ0.010 30 EGSEEDLDA 0.010 204 ELLTEVTRR 0.010 105 LENLFEALN 0.009 123KPKVYIIQA 0.009 218 LVQEGKARK 0.009 34 EDLDALEHM 0.009 81 CAFVVLMAH0.009 5 RSLEEEKYD 0.008 68 FQQAIDSRE 0.007 114 NKNCQALRA 0.007 170STVEGYIAY 0.006 165 ALHVYSTVE 0.006 83 FVVLMAHGR 0.006 176 IAYRHDQKG0.006 121 RAKPKVYII 0.005 v.2-A2-9 mers: 213P1F11 45 ALSRPWWMC 63.342 10TPFQDPLYL 2.838 38 DMIRKAHAL 1.157 20 SEAPPNPPL 0.415 44 HALSRPWWM 0.35817 YLPSEAPPN 0.343 8 GPTPFQDPL 0.260 29 WNSQDTSPT 0.224 31 SQDTSPTDM0.201 52 MCSRRGKDI 0.116 35 SPTDMIRKA 0.061 37 TDMIRKAHA 0.026 12FQDPLYLPS 0.021 14 DPLYLPSEA 0.009 32 QDTSPTDMI 0.007 27 PLWNSQDTS 0.00751 WMCSRRGKD 0.006 4 STVEGPTPF 0.004 26 PPLWNSQDT 0.004 6 VEGPTPFQD0.003 22 APPNPPLWN 0.003 39 MIRKAHALS 0.001 48 RPWWMCSRR 0.001 42KAHALSRPW 0.001 18 LPSEAPPNP 0.001 56 RGKDISWNF 0.001 15 PLYLPSEAP 0.0015 TVEGPTPFQ 0.000 3 YSTVEGPTP 0.000 30 NSQDTSPTD 0.000 43 AHALSRPWW0.000 2 VYSTVEGPT 0.000 34 TSPTDMIRK 0.000 23 PPNPPLWNS 0.000 1HVYSTVEGP 0.000 55 RRGKDISWN 0.000 46 LSRPWWMCS 0.000 25 NPPLWNSQD 0.00021 EAPPNPPLW 0.000 41 RKAHALSRP 0.000 13 QDPLYLPSE 0.000 9 PTPFQDPLY0.000 7 EGPTPFQDP 0.000 16 LYLPSEAPP 0.000 36 PTDMIRKAH 0.000 53CSRRGKDIS 0.000 50 WWMCSRRGK 0.000 33 DTSPTDMIR 0.000 47 SRPWWMCSR 0.00024 PNPPLWNSQ 0.000 28 LWNSQDTSP 0.000 11 PFQDPLYLP 0.000 54 SRRGKDISW0.000 49 PWWMCSRRG 0.000 19 PSEAPPNPP 0.000 40 IRKAHALSR 0.000 v.3-A2-9mers: 213P1F11 10 TLPSPFPYL 223.237 3 IQACRGATL 3.682 1 YIIQACRGA 0.6282 IIQACRGAT 0.226 9 ATLPSPFPY 0.022 12 PSPFPYLSL 0.005 11 LPSPFPYLS0.003 8 GATLPSPFP 0.001 7 RGATLPSPF 0.000 4 QACRGATLP 0.000 5 ACRGATLPS0.000 6 CRGATLPSP 0.000 v.4-A2-9 mers: 213P1F11 5 QEYDKSLSV 17.743 13VQPEKRTGL 15.096 50 KLVNDPRET 5.216 26 GECGQTFRL 2.409 3 KCQEYDKSL 2.00175 SISFRNSET 1.025 44 GSSVHQKLV 0.454 62 FGGGVGDIV 0.420 58 TQEVFGGGV0.223 20 GLRDENGEC 0.201 43 RGSSVHQKL 0.139 68 DIVGRDLSI 0.108 53NDPRETQEV 0.097 33 RLKEEQGRA 0.093 11 LSVQPEKRT 0.083 56 RETQEVFGG 0.01966 VGDIVGRDL 0.019 69 IVGRDLSIS 0.010 39 GRAFRGSSV 0.010 85 ASEEEKYDM0.009 10 SLSVQPEKR 0.007 84 SASEEEKYD 0.005 51 LVNDPRETQ 0.004 61VFGGGVGDI 0.004 29 GQTFRLKEE 0.003 46 SVHQKLVND 0.003 72 RFLSISFRN 0.00273 DLSISFRNS 0.002 65 GVGDIVGRD 0.002 40 RAFRGSSVH 0.002 76 ISFRNSETS0.001 23 DENGECGQT 0.001 12 SVQPEKRTG 0.001 9 KSLSVQPEK 0.001 36EEQGRAFRG 0.001 74 LSISFRNSE 0.001 18 RTGLRDENG 0.001 4 CQEYDKSLS 0.00079 RNSETSASE 0.000 30 QTFRLKEEQ 0.000 28 CGQTFRLKE 0.000 60 EVFGGGVGD0.000 19 TGLRDENGE 0.000 35 KEEQGRAFR 0.000 86 SEEEKYDMS 0.000 77SFRNSETSA 0.000 70 VGRDLSISF 0.000 83 TSASEEEKY 0.000 64 GGVGDIVGR 0.00037 EQGRAFRGS 0.000 63 GGGVGDIVG 0.000 45 SSVHQKLVN 0.000 24 ENGECGQTF0.000 81 SETSASEEE 0.000 57 ETQEVFGGG 0.000 59 QEVFGGGVG 0.000 49QKLVNDPRE 0.000 2 GKCQEYDKS 0.000 52 VNDPRETQE 0.000 67 GDIVGRDLS 0.00078 FRNSETSAS 0.000 47 VHQLKVNDP 0.000 32 FRLKEEQGR 0.000 25 NGECGQTFR0.000 42 FRGSSVHQK 0.000 38 QGRAFRGSS 0.000 17 KRTGLRDEN 0.000 21LRDENGECG 0.000 71 GRDLSISFR 0.000 34 LKEEQGRAF 0.000 82 ETSASEEEK 0.00080 NSETSASEE 0.000 1 MGKCQEYDK 0.000 8 DKSLSVQPE 0.000 7 YDKSLSVQP 0.00027 ECGQTFRLK 0.000 54 DPRETQEVF 0.000 31 TFRLKEEQG 0.000 22 RDENGECGQ0.000 48 HQKLVNDPR 0.000 14 QPEKRTGLR 0.000 41 AFRGSSVHQ 0.000 15PEKRTGLRD 0.000 55 PRETQEVPG 0.000 6 EYDKSLSVQ 0.000 16 EKRTGLRDE 0.000v.5-A2-9 mers: 213P1F11 5 ALILRVTKA 11.426 3 RLALILRVT 1.405 2 ARLALILRV0.082 6 LILRVTKAR 0.013 9 RVTKAREGS 0.003 7 ILRVTKARE 0.002 4 LALILRVTK0.001 1 GARLALILR 0.000 8 LRVTKAREG 0.000 v.6-A2-9 mers: 213P1F11 8AMNNKNCQA 3.588 1 KLENLFEAM 1.036 4 NLFEAMNNK 0.520 6 FEAMNNKNC 0.444 9MNNKNCQAL 0.237 2 LENLFEAMN 0.009 3 ENLFEAMNN 0.000 7 EAMNNKNCQ 0.000 5LFEAMNNKN 0.000

[0758] TABLE VIII Pos 1234567890 Score SeqID v.1-A2-10mers: 213P1F11 187FIQTLVDVFT 25.924 111 ALNNKNCQAL 21.362 86 LMAHGREGFL 18.753 142TVGGDEIVMV 13.997 149 VMVIKDSPQT 9.149 117 CQALRAKPKV 7.052 205LLTEVTRRMA 6.925 94 FLKGEDGEMV 5.487 119 ALRAKPKVYI 4.361 185 SCFIQTLVDV3.864 75 REDPVSCAFV 2.975 70 QAIDSREDPV 1.941 183 KGSCFIQTLV 1.589 150MVIKDSPQTI 1.552 13 DMSGARLALI 1.300 107 NLFEALNNKN 1.130 226 KTNPEIQSTL1.038 19 LALILCVTKA 0.998 218 LVQEGKARKT 0.909 63 EELEKFQQAI 0.877 159IPTYTDALHV 0.772 232 QSTLRKRLYL 0.767 103 VKLENLFEAL 0.712 134GEQRDPGETV 0.663 12 YDMSGARLAL 0.505 5 RSLEEEKYDM 0.492 143 VGGDEIVMVI0.448 162 YTDALHVYST 0.438 102 MVKLENLFEA 0.345 48 FESTMKRDPT 0.327 96KGEDGEMVKL 0.295 204 ELLTEVTRRM 0.276 140 GETVGGDEIV 0.272 182QKGSCFIQTL 0.259 190 TLVDVFTKRK 0.232 85 VLMAHGREGF 0.230 207 TEVTRRMAEA0.222 230 ETQSTLRKRL 0.220 16 GARLALILCV 0.169 27 KAREGSEEDL 0.159 157QTIPTYTDAL 0.145 163 TDALHVYSTV 0.145 37 DALEHMFRQL 0.128 79 VSCAFVVLMA0.127 200 GHILELLTEV 0.111 201 HILELLTEVT 0.106 212 RMAEAELVQE 0.102 14MSGARLALIL 0.097 29 REGSEEDLDA 0.097 78 PVSCAFVVLM 0.084 15 SGARLALILC0.075 165 ALHVYSTVEG 0.075 125 KVYIIQACRG 0.073 167 HVYSTVEGYI 0.071 104KLENLFEALN 0.063 56 PTAEQFQEEL 0.050 30 EGSEEDLDAL 0.048 175 YIAYRHDQKG0.047 41 HMFRQLRFES 0.039 209 VTRRMAEAEL 0.038 188 IQTLVDVFTK 0.034 193DVFTKRKGHI 0.033 10 EKYDMSGARL 0.029 22 ILCVTKAREG 0.025 225 RKTNPEIQST0.024 154 DSPQTIPTYT 0.020 110 EALNNKNCQA 0.019 76 EDPVSCAFVV 0.017 156PQTIPTYTDA 0.017 179 RHDQKGSCFI 0.016 122 AKPKVYIIQA 0.016 20 ALILCVTKAR0.015 18 RLALILCVTK 0.015 222 GKARKTNPEI 0.014 6 SLEEEKYDMS 0.014 21LILCVTKARE 0.013 43 FRQLRFESTM 0.012 62 QEELEKFQQA 0.012 72 IDSREDPVSC0.012 170 STVEGYIAYR 0.011 61 FQEELEKFQQ 0.011 198 RKGHILELLT 0.010 194VFTKRKGHLL 0.010 158 TIPTYTDALH 0.010 123 KPKVYIIQAC 0.009 81 CAFVVLMAHG0.009 148 IVMVIKDSPQ 0.008 84 VVLMAHGREG 0.008 77 DPVSCAFVVL 0.008 152IKDSPQTIPT 0.007 176 IAYRHDQKGS 0.006 44 RQLRFESTMK 0.006 100 GEMVKLENLF0.005 196 TKRKGHTLEL 0.005 101 EMVKLENLFE 0.004 203 LELLTEVTRR 0.004 181DQKGSCFIQT 0.004 38 ALEHMFRQLR 0.004 17 ARLALILCVT 0.004 169 YSTVEGYIAY0.003 v.2-A2-10 mers: 213P1F11 52 WMCSRRGKDI 34.660 32 SQDTSPTDMI 0.20744 AHALSRPWWM 0.142 31 NSQDTSPTDM 0.133 46 ALSRPWWMCS 0.127 45HALSRPWWMC 0.111 38 TDMIRKAHAL 0.110 18 YLPSEAPPNP 0.069 26 NPPLWNSQDT0.049 10 PTPFQDPLYL 0.036 43 KAHALSRPWW 0.020 8 EGPTPFQDPL 0.019 35TSPTDMIRKA 0.015 2 HVYSTVEGPT 0.009 23 APPNPPLWNS 0.008 14 QDPLYLPSEA0.007 13 FQDPLYLPSE 0.006 5 STVEGPTPFQ 0.005 39 DMIRKAHALS 0.004 28PLWNSQDTSP 0.003 4 YSTVEGPTPF 0.002 36 SPTDMIRKAH 0.002 29 LWNSQDTSPT0.002 21 SEAPPNPPLW 0.001 16 PLYLPSEAPP 0.001 7 VEGPTPFQDP 0.001 11TPFQDPLYLP 0.001 49 RPWWMCSRRG 0.001 19 LPSEAPPNPP 0.001 37 PTDMIRKAHA0.001 9 GPTPFQDPLY 0.000 6 GPTPFQDPLY 0.000 30 WNSQDTSPTD 0.000 22EAPPNPPLWN 0.000 40 MIRKAHALSR 0.000 20 PSEAPPNPPL 0.000 53 MCSRRGKDIS0.000 56 RRGKDISWNF 0.000 17 LYLPSEAPPN 0.000 54 CSRRGKDISW 0.000 34DTSPTDMIRK 0.000 47 LSRPWWMCSR 0.000 42 RKAHALSRPW 0.000 1 LHVYSTVEGP0.000 27 PPLWNSQDTS 0.000 15 DPLYLPSEAP 0.000 55 SRRGKDISWN 0.000 33QDTSPTDMIR 0.000 12 PRQDPLYLPS 0.000 51 WWMCSRRGKS 0.000 24 PPNPPLWNSQ0.000 3 VYSTVEGPTP 0.000 25 PNPPLWNSQD 0.000 48 SRPWWMCSRR 0.000 41IRKAHALSRP 0.000 50 PWWMCSRRGK 0.000 v.3-A2-10 mers: 213P1F11 10ATLPSPFPYL 11.472 3 IIQACRGATL 4.993 2 YIIQACRGAT 0.613 12 LPSPFPYLSL0.356 11 TLPSPFPYLS 0.283 9 GATLPSPFPY 0.006 4 IQACRGATLP 0.003 5QACRGATLPS 0.001 8 RGATLPSPFP 0.001 1 VYIIQACRGA 0.000 6 ACRGATLPSP0.000 7 CRGATLPSPF 0.000 v.4-A2-10 mers: 213P1F11 10 SLSVQPEKRT 7.452 12SVQPEKRTGL 1.869 65 GVGDIVGRDL 1.533 43 RGSSVHQKLV 0.454 4 CQEYDKSLSV0.451 52 VNDPRETQEV 0.309 84 SASEEEKYDM 0.283 76 ISFRNSETSA 0.204 57ETQEVFGGGV 0.147 74 LSISFRNSET 0.083 60 EVFGGGVGDI 0.076 25 NGECGQTFRL0.052 38 QGRAFRGSSV 0.035 2 GKCQEYDKSL 0.030 50 KLVNDPRETQ 0.026 61VFGGGVGDIV 0.016 19 TGLRDENGEC 0.016 67 GDIVGRDLSI 0.014 42 FRGSSVHQKL0.014 20 GLRDENGECG 0.011 69 IVGRDLSISF 0.011 51 LVNDPRETQE 0.009 49QKLVNDPRET 0.008 3 KCQEYDKSLS 0.007 75 SISFRNSETS 0.005 73 DLSISFRNSE0.004 5 QEYDKSLSVQ 0.004 46 SVHQKLVNDP 0.003 33 RLKEEQGRAF 0.002 35KEEQGRAFRG 0.002 30 QTFRLKEEQG 0.002 32 FRLKEEQGRA 0.002 13 VQPEKRTGLR0.001 62 FGGGVGDIVG 0.001 40 RAFRGSSVHQ 0.001 29 GQTFRLKEEQ 0.001 68DIVGRDLSIS 0.001 70 VGRDLSISFR 0.001 9 KSLSVQPEKR 0.001 83 TSASEEEKYD0.001 79 RNSETSASEE 0.000 9 KSLSVQPEKR 0.000 83 TSASEEEKYD 0.000 79RNSETSASEE 0.000 86 SEEEKYDMSG 0.000 56 RETQEVFGGG 0.000 59 QEVFGGGVGD0.000 37 EQGRAFRGSS 0.000 45 SSVHQKLVND 0.000 28 CGQTFRLKEE 0.000 63GGGVGDIVGR 0.000 18 RTGLRDENGE 0.000 44 GSSVHQKLVN 0.000 11 LSVQPEKRTG0.000 24 ENGECGQTFR 0.000 66 VGDIVGRDLS 0.000 72 RDLSISFRNS 0.000 81SETSASEEEK 0.000 26 GECGQTFRLK 0.000 23 DENGECGQTF 0.000 85 ASEEEKYDMS0.000 22 RDENGECGQT 0.000 54 DPRETQEVFG 0.000 34 LKEEQGRAFR 0.000 36EEQGRAFRGS 0.000 82 ETSASEEEKY 0.000 64 GGVGDIVGRD 0.000 27 ECGQTFRLKE0.000 58 TQEVFGGGVG 0.000 71 GRDLSISFRN 0.000 1 MGKCQEYDKS 0.000 53NDPRETQEVF 0.000 17 KRTGLRDENG 0.000 78 FRNSETSASE 0.000 47 VHQKLVNDPR0.000 7 YDKSLSVQPE 0.000 14 QPEKRTGLRD 0.000 21 LRDENGECGQ 0.000 39GRAFRGSSVH 0.000 77 SFRNSETSAS 0.000 80 NSETSASEEE 0.000 41 AFRGSSVHQK0.000 48 HQKLVNDPRE 0.000 8 DKSLSVQPEK 0.000 31 TFRLKEEQGR 0.000 16EKRTGLRDEN 0.000 55 PRETQEVFGG 0.000 15 PEKRTGLFDE 0.000 6 EYDKSLSVQP0.000 v.5-A2-10 mers: 213P1F11 5 LALILRVTKA 0.998 2 GARLALILRV 0.169 6ALALRVTKAR 0.015 4 RLALILRVTK 0.015 7 LILRVTKARE 0.013 8 ILRVTKAREG0.002 3 ARLALILRVT 0.001 1 SGARLALILR 0.000 10 RVTKAREGSE 0.000 9LRVTKAREGS 0.000 v.6-A2-10mers: 213P1F11 9 AMNNKNCQAL 15.428 5NLFEAMNNKN 1.130 1 VKLENLFEAM 0.166 2 KLENLFEAMN 0.063 8 EAMNNKNCQA0.019 3 LENLFEAMNN 0.002 7 FEAMNNKNCQ 0.001 6 LFEAMNNKNC 0.000 10MNNKNCQALR 0.000 4 ENLFEAMNNK 0.000

[0759] TABLE IX Pos 123456789 Score SeqID v.1-A3-9mers: 213P1F11 107NLFEALNNK 225.000 190 TLVDVFTKR 27.000 45 QLRFESTMK 20.000 189 QTLVDVFTK13.500 125 KVYIIQACR 9.000 167 HVYSTVEGY 6.000 204 ELLTEVTRR 5.400 104KLENLFEAL 5.400 218 LVQEGKARK 3.000 191 LVDVFTKRK 3.000 171 TVEGYIAYR2.700 119 ALRAKPKVY 2.000 86 LMAHGREGF 2.000 175 YIAYRHDQK 2.000 59EQFQEELEK 1.800 6 SLEEEKYDM 0.900 217 ELVQEGKAR 0.900 101 EMVKLENLF0.900 20 ALILCVTKA 0.900 170 STVEGYIAY 0.900 83 FVVLMAHGR 0.600 35DLDALEHMF 0.600 187 FIQTLVDVF 0.600 64 ELEKFQQAI 0.540 13 DMSGARLAL0.540 21 LILCVTKAR 0.450 19 LALILCVTK 0.300 117 CQALRAKPK 0.300 18RLALILCVT 0.225 111 ALNNKNCQA 0.200 3 NPRSLEEEK 0.200 38 ALEHMFRQL 0.180158 TIPTYTDAL 0.180 145 GDEIVMVIK 0.135 96 KGEDGEMVK 0.120 129 IQACRGEQR0.120 202 ILELLTEVT 0.100 233 STLRKRLYL 0.090 94 FLKGEDGEM 0.090 234TLRKRLYLQ 0.090 215 EAELVQEGK 0.090 121 RAKPKVYII 0.081 201 HILELLTEV0.068 88 AHGREGFLK 0.060 46 LRFESTMKR 0.060 165 ALHVYSTVE 0.060 151VIKDSPQTT 0.060 212 RMAEAELVQ 0.060 142 TVGGDEIVM 0.060 123 KPKVYIIQA0.054 205 LLTEVTRRM 0.045 81 CAFVVLMAH 0.045 228 NPEIQSTLR 0.040 39LEHMFRQLR 0.036 226 KTNPEIQST 0.034 195 FTKRKGHIL 0.030 149 VMVIKDSPQ0.030 44 RQLRFESTM 0.027 144 GGDEIVMVI 0.024 157 QTIPTYTDA 0.022 31GSEEDLDAL 0.020 71 AIDSREDPV 0.020 51 TMKRDPTAE 0.020 22 ILCVTKARE 0.02067 KFQQAIDSR 0.018 115 KNCQALRAK 0.018 57 TAEQFQEEL 0.018 203 LELLTEVTR0.018 229 PEIQSTLRK 0.018 16 GARLALTLC 0.018 80 SCAFVVLMA 0.018 230EIQSTLRKR 0.018 223 KARKTNPEI 0.018 78 PVSCAFVVL 0.018 193 DVFTKRKGH0.015 50 STMKRDPTA 0.015 150 MVIKDSPQT 0.015 41 HMFRQLRFE 0.015 75REDPVSCAF 0.013 97 GEDGEMVKL 0.012 100 GEMVKLENL 0.012 160 PTYTDALHV0.010 53 KRDPTAEQF 0.009 79 VSCAFVVLM 0.009 231 IQSTLRKRL 0.009 208EVTRRMAEA 0.009 154 DSPQTIPTY 0.009 197 KRKGHILEL 0.008 183 KGSCFIQTL0.008 36 LDALEHMFR 0.008 113 NNKNCQALR 0.008 141 ETVGGDEIV 0.007 161TYTDALHVY 0.006 140 GETVGGDEI 0.005 60 QEQEELEKE 0.005 188 IQTLVDVFT0.005 184 GSCFIQTLV 0.005 148 IVMVIKDSP 0.005 14 MSGARLALI 0.005 102MVKLENLFE 0.004 v.2-A3-9 mers: 213P1F11 45 ALSRPWWMC 0.900 34 TSPTDMIRK0.300 38 DMIRKAHAL 0.270 4 STVEGPTPF 0.225 48 RPWWMCSRR 0.200 33DTSPTDMIR 0.180 8 GPTPFQDPL 0.081 10 TPFQDPLYL 0.060 1 HVYSTVEGP 0.03017 YLPSEAPPN 0.020 27 PLWNSQDTS 0.020 9 PTPFQDPLY 0.020 47 SRPWWMCSR0.018 15 PLYLPSEAP 0.015 56 RGKDISWNF 0.009 44 HALSRPWWM 0.009 40IRKAHALSR 0.008 51 WMSCRRGKD 0.006 31 SQDTSPTDM 0.006 5 TVEGPTPFQ 0.00520 SEAPPNPPL 0.004 39 MIRKAHALS 0.004 12 FQDPLYLPS 0.004 50 WWMCSRRGK0.003 52 MCSRRGKDI 0.003 46 LSRPWWMCS 0.002 32 QDTSPTDMI 0.001 14DPLYLPSEA 0.001 21 EAPPNPPLW 0.001 36 PTDMIRKAH 0.001 22 APPNPPLWN 0.00142 KAHALSRPW 0.001 25 NPPLWNSQD 0.001 54 SRRGKDISW 0.001 23 PPNPPLWNS0.000 18 LPSEAPPNP 0.000 37 TDMIRKAHA 0.000 35 SPTDMIRKA 0.000 6VEGPTPFQD 0.000 29 WNSQDTSPT 0.000 43 AHALSRPWW 0.000 53 CSRRGKDIS 0.00026 PPLWNSQDT 0.000 3 YSTVEGPTP 0.000 30 NSQDTSPTD 0.000 13 QDPLYLPSE0.000 16 LYLPSEAPP 0.000 2 VYSTVEGPT 0.000 55 RRGKDISWN 0.000 41RKAHALSRP 0.000 7 EGPTPFQDP 0.000 28 LWNSQDTSP 0.000 19 PSEAPPNPP 0.00011 PFQDPLYLP 0.000 24 PNPPLWNSQ 0.000 49 PWWMCSRRG 0.000 v.3-A3-9 mers:213P1F11 10 TLPSPFPYL 2.700 9 ATLPSPFPY 1.350 3 IQACRGATL 0.018 11LPSPFPYLS 0.005 1 YIIQACRGA 0.003 2 IIQACRGAT 0.003 7 RGATLPSPF 0.002 5ACRGATLPS 0.001 12 PSPFPYLSL 0.001 8 GATLPSPFP 0.001 4 QACRGATLP 0.000 6CRGATLPSP 0.000 v.4-A3-9 mers: 213P1F11 10 SLSVQPEKR 4.000 9 KSLSVQPEK0.675 82 ETSASEEEK 0.300 48 HQKLVNDPR 0.180 20 GLRDENGEC 0.180 33RLKEEQGRA 0.090 68 DIVGRDLSI 0.081 42 FRGSSVHQK 0.060 1 MGKCQEYDK 0.06050 KLVNDPRET 0.045 64 GGVGDIVGR 0.041 3 KCQEYDKSL 0.041 35 KEEQGRAFR0.036 13 VQPEKRTGL 0.027 26 GECGQTFRL 0.024 83 TSASEEEKY 0.020 71GRDLSISFR 0.018 27 ECGQTFRLK 0.018 14 QPEKRTGLR 0.012 40 RAFRGSSVH 0.01075 SISFRNSET 0.010 54 DPRETQEVF 0.009 65 GVGDIVGRD 0.008 32 FRLKEEQGR0.006 69 IVGRDLSIS 0.006 5 QEYDKSLSV 0.006 58 TQEVFGGGV 0.005 30QTFRLKEEQ 0.005 85 ASEEEKYDM 0.005 60 EVFGGGVGD 0.005 70 VGRDLSISF 0.00425 NGECGQTFR 0.004 73 DLSISFRNS 0.004 51 LVNDPRETQ 0.003 46 SVHQKLVND0.003 24 ENGECGQTF 0.002 44 GSSVHQKLV 0.002 29 GQTFRLKEE 0.001 4CQEYDKSLS 0.001 18 RTGLRDENG 0.001 76 ISFRNSETS 0.001 43 RGSSVHQKL 0.00161 VFGGGVGDI 0.001 57 ETQEVFGGG 0.001 39 GRAFRGSSV 0.001 11 LSVQPEKRT0.001 56 RETQEVFGG 0.001 62 FGGGVGDIV 0.000 74 LSISFRNSE 0.000 12SVQPEKRTG 0.000 34 LKEEQGRAF 0.000 45 SSVHQKLVN 0.000 53 NDPRETQEV 0.00077 SFRNSETSA 0.000 67 GDIVGRDLS 0.000 86 SEEEKYDMS 0.000 84 SASEEEKYD0.000 72 RDLSISFRN 0.000 2 GKCQEYDKS 0.000 63 GGGVGDIVG 0.000 28CGQTFRLKE 0.000 37 EQGRAFRGS 0.000 80 NSETSASEE 0.000 66 VGDIVGRDL 0.00017 KRTGLRDEN 0.000 36 EEQGRAFRG 0.000 52 VNDPRETQE 0.000 79 RNSETSASE0.000 47 VHQKLVNDP 0.000 81 SETSASEEE 0.000 23 DENGECGQT 0.000 78FRNSETSAS 0.000 38 QGRAFRGSS 0.000 21 LRDENGECG 0.000 19 TGLRDENGE 0.00049 QKLVNDPRE 0.000 41 AFRGSSVHQ 0.000 59 QEVFGGGVG 0.000 31 TFRLKEEQG0.000 7 YDKSLSVQP 0.000 22 RDENGECGQ 0.000 8 DKSLSVQPE 0.000 15PEKRTGLRD 0.000 6 EYDKSLSVQ 0.000 55 PRETQEVFG 0.000 16 EKRTGLRDE 0.000v.5-A3-9 mers: 213P1F11 5 ALILRVTKA 0.900 6 LILRVTKAR 0.450 1 GARLALILR0.360 4 LALILRVTK 0.300 3 RLALILRVT 0.022 7 ILRVTKARE 0.020 9 RVTKAREGS0.004 2 ARLALILRV 0.001 8 LRVTKAREG 0.000 v.6-A3-9 mers: 213P1F11 4NLFEAMNNK 225.000 1 KLENLFEAM 1.800 8 AMNNKNCQA 0.200 9 MNNKNCQAL 0.2006 FEAMNNKNC 0.000 2 LENLFEAMN 0.000 7 EAMNNKNCQ 0.000 3 ENLFEAMNN 0.0005 LFEAMNNKN 0.000

[0760] TABLE X Pos 1234567890 Score SeqID v.1-A3-10 mers 190 TLVDVFTKRK45.000 18 RLALILCVTK 20.000 38 ALEHMFRQLR 12.000 217 ELVQEGKARK 9.000 45QLRFESTMKR 8.000 188 IQTLVDVFTK 5.400 20 ALILCVTKAR 4.500 202 ILELLTEVTR4.000 85 VLMAHGREGF 3.000 35 DLDALEHMFR 2.400 170 STVEGYIAYR 2.025 189QTLVDVFTKR 1.350 87 MAHGREGFLK 0.900 44 RQLRFESTMK 0.900 119 ALRAKPKVYI0.900 41 HMFRQLRFES 0.600 111 ALNNKNCQAL 0.600 13 DMSGARLALI 0.405 128IIQACRGEQR 0.400 228 NPEIQSTLRK 0.400 94 FLKGEDGEMV 0.300 144 GGDEIVMVIK0.203 157 QTIPTYTDAL 0.203 226 KTNPEIQSTL 0.203 86 LMAHGREGFL 0.180 104KLENLFEALN 0.180 107 NLFEALNNKN 0.150 160 PTYTDALHVY 0.150 149VMVIKDSPQT 0.150 59 EQFQEELEKF 0.135 214 AEAELVQEGK 0.135 167 HVYSTVEGYI0.135 171 TVEGYIAYRH 0.135 58 AEQFQEELEK 0.120 116 NCQALRAKPK 0.100 174GYTAYRHDQK 0.090 150 MVTKDSPQTI 0.090 102 MVKLEHLFEA 0.090 95 LKGEDGEMVK0.060 6 SLEEEKYDMS 0.060 203 LELLTEVTRR 0.054 162 YTDALHVYST 0.045 142TVGGDEIVMV 0.045 212 RMAEAELVQE 0.045 169 YSTVEGYIAY 0.040 2 SNPRSLEEEK0.040 3 NPRSLEEEKY 0.040 118 QALRAKPKVY 0.030 125 KVYIIQACRG 0.030 205LLTEVTRRMA 0.030 51 TMKRDPTAEQ 0.030 209 VTRRMAEAEL 0.030 193 DVFTKRKGHI0.027 153 KDSPQTIPTY 0.027 106 ENLFEALNNK 0.027 27 KAREGSEEDL 0.027 100GEMVKLENLF 0.027 201 HILELLTEVT 0.022 158 TIPTYTDALH 0.020 165ALHVYSTVEG 0.020 166 LHVYSTVEGY 0.018 16 GARLALILCV 0.018 78 PVSCAFVVLM0.018 101 EMVKLENIFE 0.018 187 FIQTLVDVFT 0.015 185 SCFIQTLVDV 0.015 123KPKVYIIQAC 0.013 141 ETVGGDEIVM 0.013 204 ELLTEVTRRM 0.013 56 PTAEQFQEEL0.013 231 IQSTLRKRLY 0.012 227 TNPEIQSTLR 0.012 39 LEHMFRQLRF 0.012 186CFIQTLVDVF 0.009 79 VSCAFVVLMA 0.009 66 EKFQQAIDSR 0.009 216 AELVQEGKAR0.009 19 LALTLCVTKA 0.009 80 SCAFVVLMAH 0.009 230 ETQSTLRKRL 0.009 77DPVSCAFVVL 0.008 181 DQKGSCFIQT 0.008 112 LNNKNCQALR 0.008 233STLRKRLYLQ 0.007 5 RSLEEEKYDM 0.007 197 KRKGHILELL 0.006 82 AFVVLMAHGR0.006 14 MSGARLALIL 0.006 232 QSTLRKRLYL 0.006 117 CQALRAKPKV 0.006 64ELEKFQQATD 0.006 143 VGGDEIVMVT 0.005 120 LRAKPKVYII 0.005 103VKLENLFEAL 0.004 159 IPTYTDALHV 0.004 71 AIDSREDPVS 0.004 63 EELEKFQQAI0.004 74 SREDPVSCAF 0.003 114 NKNCQALRAK 0.003 148 IVMVIKDSPQ 0.003v.2-A3-10 mers: 213P1F11 34 DTSPTDMIRE 1.350 40 MIRKAHALSR 0.800 52WMCSRRGKDI 0.300 46 ALSRPWWMCS 0.240 9 GPTPFQDPLY 0.180 47 LSRPWWNCSR0.135 32 SQDTSPTDMI 0.027 2 HVYSTVEGPT 0.022 18 YLPSEAPPNP 0.020 39DMIRKAHALS 0.018 45 HALSRPWWMC 0.013 16 PLYLPSEAPP 0.010 4 YSTVEGPTPF0.010 28 PLWNSQDTSP 0.010 56 RRGKDISWNF 0.009 6 TVEGPTPFQD 0.009 33QDTSPTDMIR 0.008 11 TPFQDPLYLP 0.007 10 PTPFQDPLYL 0.006 43 KAHALSRPWW0.006 13 FQDPLYLPSE 0.004 48 SRPWWMCSRR 0.004 5 STVEGPTPFQ 0.003 23APPNPPLWNS 0.003 54 CSRRGKDISW 0.002 36 SPTDMIRKAH 0.002 50 PWWMCSRRGK0.001 31 NSQDTSPTDM 0.001 37 PTDMIRKAHA 0.001 26 NPPLWNSQDT 0.001 38TDMIRKAHAL 0.001 21 SEAPPNPPLW 0.001 44 AHALSRPWWM 0.001 8 EGPTPFQDPL0.001 20 PSEAPPNPPL 0.000 19 LPSEAPPNPP 0.000 7 VEGPTPFQDP 0.000 53MCSRRGKDIS 0.000 22 EAPPNPPLWN 0.000 14 QDPLYLPSEA 0.000 35 TSPTDMIRKA0.000 15 DPLYLPSEAP 0.000 29 LWNSQDTSPT 0.000 49 RPWWMCSRRG 0.000 1LHVYSTVEGP 0.000 27 PPLWNSQDTS 0.000 55 SRRGKDISWN 0.000 17 LYLPSEAPPN0.000 30 WNSQDTSPTD 0.000 24 PPNPPLWNSQ 0.000 41 IRKAHALSRP 0.000 3VYSTVEGPTP 0.000 42 RKAHALSRPW 0.000 25 PNPPLWNSQD 0.000 51 WWMCSRRGKD0.000 12 PFQDPLYLPS 0.000 v.3-A3-10 mers: 213P1F11 11 TLPSPFPYLS 0.360 9GATLPSPFPY 0.360 10 ATLPSPFPYL 0.304 3 IIQACRGATL 0.060 12 LPSPFPYLSL0.027 2 YIIQACRGAT 0.005 7 CRGATLPSPF 0.002 5 QACRGATLSP 0.001 4IQACRGATLP 0.001 6 ACRGATLPSP 0.000 8 RGATLPSPFP 0.000 1 VYIIQACRGA0.000 v.4-A3-10 mers: 213P1F11 69 IVGRDLSISF 0.400 33 RLKEEQGRAF 0.30050 KLVNDPRETQ 0.135 60 EVFGGGVGDI 0.121 41 AFRGSSVHQK 0.090 12SVQPEKRTGL 0.090 9 KSLSVQPEKR 0.090 26 GECGQTFRLK 0.081 10 SLSVQPEKRT0.075 20 GLRDENGECG 0.060 81 SETSASEEEK 0.060 82 ETSASEEEKY 0.060 13VQPEKRTGLR 0.054 65 GVGDIVGRDL 0.027 63 GGGVGDIVGR 0.018 73 DLSISFRNSE0.018 4 CQEYDKSLSV 0.012 84 SASEEEKYDM 0.009 8 DKSLSVQPEK 0.009 70VGRDLSISFR 0.006 47 VHQKLVNDPR 0.006 34 LKEEQGRAFR 0.006 46 SVHQKLVNDP0.006 67 GDIVGRDLSI 0.005 76 ISFRNSETSA 0.005 30 QTFRLKEEQG 0.005 57ETQEVFGGGV 0.004 68 DIVGRDLSIS 0.004 75 SISFRNSETS 0.004 31 TFRLKEEQGR0.004 24 ENGECGQTRF 0.004 23 DENGECGQTF 0.003 2 GKCQEYDKSL 0.003 51LVNDPRETQE 0.003 53 NDPRETQEVG 0.002 25 NGECGQTFRL 0.002 29 GQTFRLKEEQ0.002 3 KCQEYDKSLS 0.002 40 RAFRGSSVHQ 0.001 18 RTGLRDENGE 0.001 42FRGSSVHQKL 0.001 74 LSISFRNSET 0.001 44 GSSVHQKLVN 0.001 39 GRAFRGSSVN0.001 48 HQKLVNDPRE 0.001 52 VNDPRETQEV 0.001 35 KEEQGRAFRG 0.001 86SEEEKYDMSG 0.001 61 VFGGGVGDIV 0.000 5 QEYDKSLSVQ 0.000 14 QPEKRTGLRD0.000 27 ECGQTFRLKE 0.000 37 EQGRAFRGSS 0.000 85 ASEEEKYDMS 0.000 71GRDLSISFRN 0.000 45 SSVHQKLVND 0.000 38 QGRAFRGSSV 0.000 64 GGVGDIVGRD0.000 58 TQEVFGGGVG 0.000 80 NSETSASEEE 0.000 43 RGSSVHQKLV 0.000 17KRTGLRDENG 0.000 32 FRLKEEQGRA 0.000 19 TGLRDENGEC 0.000 54 DPRETQEVFG0.000 59 QEVFGGGVGD 0.000 56 RETQEVFGGG 0.000 79 RNSETSASEE 0.000 62FGGGVGDIVG 0.000 7 YDKSLSVQPE 0.000 83 TSASEEEKYD 0.000 77 SFRNSETSAS0.000 66 VGDIVGRDLS 0.000 1 MGKCQEYDKS 0.000 21 LRDENGECGQ 0.000 22RDENGECGQT 0.000 78 FRNSETSASE 0.000 55 PRETQEVFGG 0.000 72 RDLSISFRNS0.000 36 EEQGRAFRGS 0.000 28 CGQTFRLKEE 0.000 11 LSVQPEKRTG 0.000 49QKLVNDPRET 0.000 6 EYDKSLSVQP 0.000 16 EYDKSLSVQP 0.000 15 PEKRTGLRDE0.000 v.5-A3-10 mers: 213P1F11 4 RLALILRVTK 20.000 6 ALILRVTKAR 4.500 2GARLALILRV 0.018 1 SGARLALILR 0.012 5 LALILRVTKA 0.009 7 LILRVTKARE0.003 8 ILRVTKAREG 0.002 10 RVTKAREGSE 0.001 9 LRVTKAREGS 0.000 3ARLALILRVT 0.000 v.6-A3-10 mers: 213P1F11 9 AMNNKNCQAL 0.600 2KLENLFEAMN 0.180 5 NLFEAMNNKN 0.150 4 ENLFEAMNNK 0.027 10 MNNKNCQALR0.008 1 VKLENLFEAM 0.001 8 EAMNNKNCQA 0.001 3 LENLFEAMNN 0.000 6LFEAMNNKNC 0.000 7 FEAMNNKNCQ 0.000

[0761] TABLE XI Pos 123456789 Score SeqID v.1-A11-9 mers:213P1F11 189QTLVDVFTK 4.500 125 KVYIIQACR 2.400 218 LVQEGKARK 2.000 191 LVDVFTKRK1.000 107 NLFEALNNK 0.800 59 EQFQEELEK 0.720 83 FVVLMAHGR 0.600 171TVEGYIAYR 0.400 45 QLRFESTMK 0.400 175 YIAYRHDQK 0.400 19 LALILCVTK0.300 117 CQALRAKPK 0.300 3 NPRSLEEEK 0.200 96 KGEDGEMVK 0.120 129IQACRGEQR 0.120 190 TLVDVFTKR 0.120 67 KFQQAIDSR 0.120 88 AHGREGFLK0.060 145 GDEIVMVIK 0.060 215 EAELVQEGK 0.060 21 LILCVTKAR 0.060 142TVGGDEIVM 0.040 228 NPEIQSTLR 0.040 167 HVYSTVEGY 0.040 204 ELLTEVTRR0.036 233 STLRKRLYL 0.030 170 STVEGYIAY 0.030 44 RQLRFESTM 0.027 50STMKRDPTA 0.020 217 ELVQEGKAR 0.018 229 PETQSTLRK 0.018 203 LELLTEVTR0.018 46 LRFESTMKR 0.016 157 QTIPTYTDA 0.015 115 KNCQALRAK 0.012 121RAKPKVYII 0.012 39 LEIIMFRQLR 0.012 104 KLEHLFEAL 0.012 123 KPKVYIIQA0.012 11 KYDMSGARL 0.012 195 FTKRKOHIL 0.010 36 LDALEHMFR 0.008 81CAFVVLMAH 0.008 113 NNKNCQALR 0.008 6 SLEEEKYDM 0.008 201 HILELLTEV0.006 193 DVFTKRKGH 0.006 20 ALILCVTKA 0.006 223 KARKTNPEI 0.006 208EVTRRMAEA 0.006 141 ETVGGDEIV 0.005 94 FLKGEDGEM 0.004 80 SCAFVVLMA0.004 111 ALNNKNCQA 0.004 102 MVKLENLFE 0.004 86 LMAHGREGF 0.004 148IVMVIKDSP 0.004 160 PTYTDALHV 0.004 187 FIQTLVDVF 0.004 151 VIKDSPQTI0.004 161 TYTDALHVY 0.004 71 AIDSREDPV 0.004 168 VYSTVEGYI 0.004 158TIPTYTDAL 0.004 100 GEMVKLENL 0.004 226 KTNPEIQST 0.003 150 MVIKDSPQT0.003 118 QALPAKPKV 0.003 186 CFIQTLVDV 0.003 84 VVLMAHGRE 0.003 231IQSTLRKRL 0.003 77 DPVSCAFVV 0.003 212 RMAEAELVQ 0.002 13 DMSGARLAL0.002 10 EKYDMSGAR 0.002 230 EIQSTLRKR 0.002 57 TAEQFQEEL 0.002 159IPTYTDALH 0.002 60 QFQEELEKF 0.002 119 ALRAKPKVY 0.002 87 MAHGREGFL0.002 194 VFTKRKGHI 0.002 78 PVSCAFVVL 0.002 24 CVTKAREGS 0.002 174GYIAYRHDQ 0.002 135 EQRDPGETV 0.002 75 REDPVSCAF 0.002 101 EMVKLENLF0.002 140 GETVGGDEI 0.002 97 GEDGEMVKL 0.002 16 GARLALILC 0.001 211RRMAEAELV 0.001 197 KRKGHILEL 0.001 144 GGDEIVMVI 0.001 18 RLALILCVT0.001 64 ELEKFQQAI 0.001 172 VEGYIAYRH 0.001 35 DLDALEHMF 0.001 162YTDALHVYS 0.001 206 LTEVTRRMA 0.001 v.2-A11-9 mers 48 RPWWMCSRR 0.240 33DTSPTDMIR 0.120 34 TSPTDMIRK 0.040 4 STVEGPTPF 0.015 40 IRKAHALSR 0.00810 TPFQDPLYL 0.008 31 SQDTSPTDM 0.006 44 HALSRPWWM 0.006 8 GPTPFQDPL0.006 50 WMMCSRRGK 0.004 1 HVYSTVEGP 0.004 47 SRPWWMCSR 0.004 5TVEGPTPFQ 0.002 38 DMIRKAHAL 0.002 56 RGKDISWNF 0.001 12 FQDPLYLPS 0.00152 MCSRRGKDI 0.001 9 PTPFQDPLY 0.001 14 DPLYLPSEA 0.001 45 ALSRPWWMC0.001 16 LYLPSEAPP 0.001 42 KAHALSRPW 0.001 21 EAPPNPPLW 0.001 20SEAPPNPPL 0.001 36 PTDMIRKAH 0.001 2 VYSTVEGPT 0.000 22 APPNPPLWN 0.00017 YLPSEAPPN 0.000 37 TDMIRKAHA 0.000 39 MIRKAHALS 0.000 51 WMCSRRGKD0.000 54 SRRGKDIWA 0.000 25 NPPLWNSQD 0.000 32 QDTSPTDMI 0.000 18LPSEAPPNP 0.000 35 SPTDMIRKA 0.000 43 ANALSRPWW 0.000 6 VEGPTPFQD 0.00015 PLYLPSEAP 0.000 27 PLWNSQDTS 0.000 41 RKAHALSRP 0.000 55 RRGKLISWN0.000 29 WNSQDTSPT 0.000 11 PFQDPLYLP 0.000 46 LSRPWWMCS 0.000 23PPNPPLWNS 0.000 26 PPLWNSQDT 0.000 53 CSRRGKDIS 0.000 30 NSQDTSPTD 0.00013 QDPLYLPSE 0.000 3 YSTVEGPTP 0.000 28 LWNSQDTSP 0.000 7 EGPTPFQDP0.000 24 PNPPLWNSQ 0.000 19 PSEAPPNPP 0.000 49 PWWMCSRRG 0.000 v.3-A11-9mers 9 ATLPSPFPY 0.045 3 IQACRGATL 0.006 10 TLPSPFPYL 0.004 8 GATLPSPFP0.001 1 YIIQACRGA 0.001 7 RGATLPSPF 0.001 11 LPSPFPYLS 0.000 5 ACRGATLPS0.000 2 IIQACRGAT 0.000 4 QACRGATLP 0.000 12 PSPFPYLSL 0.000 6 CRGATLPSP0.000 v.4-A11-9 mers: 213P1F11 82 ETSASEEEK 0.300 48 HQKLVNDPR 0.120 9KSLSVQPEK 0.090 10 SLSVQPEKR 0.080 1 MGKCQEYDK 0.040 14 QPEKRTGLR 0.04035 KEEQGRAFR 0.036 42 FRGSSVHQK 0.020 64 GGVGDIVGR 0.018 71 GRDLSISFR0.012 33 RLKEEQGRA 0.012 40 RAFRGSSVH 0.012 32 FRLKEEQGR 0.006 65GVGDIVGRD 0.006 27 ECGQTFRLK 0.006 58 TQEVFGGGV 0.006 13 VQPEKRTGL 0.00626 GECGQTFRL 0.005 25 NGECGQTRF 0.004 68 DIVGRDLSI 0.004 3 KCQEYDKSL0.003 18 RTGLRDENG 0.003 5 QEYDKSLSV 0.002 77 SFRNSETSA 0.002 46SVHQKLVND 0.002 51 LVNDPRETQ 0.002 30 QTFRLKEEQ 0.002 69 IVGRDLSIS 0.00261 VFGGGVGDI 0.002 20 GLRDENGEC 0.001 60 EVFGGGVGD 0.001 29 GQTFRLKEE0.001 43 RGSSVHQKL 0.001 4 CQEYDKSLS 0.001 39 GRAFRGSSV 0.001 54DPRETQEVF 0.001 56 RETQEVFGG 0.001 75 SISFRNSET 0.000 85 ASEEEKYDM 0.00070 VGRDLSISF 0.000 44 GSSVHQKLV 0.000 57 ETQEVFGGG 0.000 72 RDLSISFRN0.000 41 AFRGSSVHQ 0.000 53 NDPRETQEV 0.000 31 TFRLKEEQG 0.000 83TSASEEEKY 0.000 62 FGGGVGDIV 0.000 12 SVQPEKRTG 0.000 50 KLVNDPRET 0.00079 RNSETSASE 0.000 63 GGGVGDIVG 0.000 6 EYDKSLSVQ 0.000 24 ENGECGQTF0.000 84 SASEEEKYL 0.000 67 GDIVGRDLS 0.000 59 QEVFGGGVG 0.000 17KRTGLRDEN 0.000 45 SSVHQKLVN 0.000 22 RDENGECGQ 0.000 2 GKCQEYDKS 0.00086 SEEEKYDMS 0.000 81 SETSASEEE 0.000 36 EEQGRAFRG 0.000 52 VNDPRETQE0.000 28 CGQTFRLKE 0.000 76 ISFRNSETS 0.000 74 LSISFRNSE 0.000 49QKLVNDPRE 0.000 19 TGLRDENGE 0.000 47 VHQKLVNDP 0.000 66 VGEIVGRDL 0.00038 QGRAFRGSS 0.000 34 LKEEQGRAF 0.000 80 NSETSASEE 0.000 7 YDKLSLVQP0.000 78 FRNSETSAS 0.000 21 LRDENGECG 0.000 37 EQGRAFRGS 0.000 23DENGECGQT 0.000 11 LSVQPEKRT 0.000 15 PEFKRGLRD 0.000 73 DLSISFRNS 0.0008 DKSLSVQPE 0.000 55 PRETQEVFG 0.000 16 EKRTGLRDE 0.000 v.5-A11-9 mers:213P1F11 4 LALILRVTK 0.300 1 GARLALILR 0.240 6 LILRVTKAR 0.060 9RVTKAREGG 0.006 5 ALILRVTKA 0.006 2 ARLALILRV 0.001 7 ILRVTKARE 0.000 3RLALILRVT 0.000 8 LRVTKAREG 0.000 v.6-A11-9 mers: 213P1F11 4 NLFEAMNNK0.800 1 KLENLFEAM 0.012 8 AMNNKNCQA 0.004 9 MNNKNCQAL 0.000 5 LFEAMNNKN0.000 7 EAMNNKNCQ 0.000 2 LENLFEAMN 0.000 3 ENLFEAMNN 0.000 6 FEAMNNKNC0.000

[0762] TABLE XII Pos 1234567890 Score SeqID v.1-A11-10 mers: 213P1F11 44RQLRFESTMK 2.700 174 GYIAYRHDQK 1.800 188 IQTLVDVFTK 1.800 18 RLALILCVTK1.200 87 MAHGREGFLK 0.600 228 NPEIQSTLRK 0.400 190 TLVDVFTKRK 0.300 189QTLVDVFTKR 0.300 170 STVEGYIAYR 0.300 217 ELVQEGKARK 0.180 45 QLRFESTMKR0.160 58 AEQEQEELEK 0.120 116 NCQALRAKPK 0.100 38 ALEHMFRQLR 0.080 202ILELLTEVTR 0.080 128 IIQACRGEQR 0.080 144 GGDETVMVIK 0.060 102MVKLENLFEA 0.060 214 AEAELVQEGK 0.060 82 AFVVLMAHGR 0.060 20 ALTLCVTKAR0.060 35 DLDALEHMFR 0.048 171 TVEGYIAYRH 0.040 2 SNPRSLEEEK 0.040 95LKGEDGEMVK 0.040 167 HVYSTVEGYI 0.040 150 MVIKDSPQTI 0.030 226KTNPEIQSTL 0.030 142 TVGGDEIVMV 0.020 203 LELLTEVTRR 0.018 106ENLFEALNNK 0.018 157 QTIPTYTDAL 0.015 193 DVFTKRKGHI 0.012 16 GARLALILCV0.012 125 KVYIIQACRG 0.012 209 VTRRMAEAEL 0.010 93 GFLKGEDGEM 0.009 216AELVQEGKAR 0.009 141 ETVGGDEIVM 0.009 168 VYSTVEGYIA 0.008 112LNNKNCQALR 0.008 85 VLMAHGREGF 0.008 227 TNPEIQSTLR 0.008 27 KAREGSEEDL0.006 117 CQALRAKPKV 0.006 111 ALNNKNCQAL 0.004 80 SCAFVVLMAH 0.004 185SCFIQTLVDV 0.004 94 FLKGEDGEMV 0.004 86 LMAHGREGFL 0.004 158 TIPTYTDALH0.004 119 ALRAKPKVYI 0.004 159 IPTYTDALHV 0.004 148 IVMVIKDSPQ 0.004 59EQFQEELEKF 0.004 9 EEKYDMSGAR 0.004 29 REGSEEDLDA 0.004 100 GEMVKLENLF0.004 83 FVVLMAHGRE 0.003 233 STLRKRLYLQ 0.003 19 LALILCVTKA 0.003 186CFIQTLVDVF 0.003 70 QAIDSREDPV 0.003 41 HMFRQLRFES 0.002 66 EKFQQAIDSR0.002 114 NKNCQALRAK 0.002 50 STMKRDPTAE 0.002 3 NPRSLEEEKY 0.002 162YTDALHVYST 0.002 206 LTEVTRRMAE 0.002 195 FTKRKGHILE 0.002 194VFTKRKGHIL 0.002 24 CVTKAREGSE 0.002 78 PVSCAFVVLM 0.002 160 PTYTDALHVY0.002 5 RSLEEEKYDM 0.002 61 FQEELEKFQQ 0.002 75 REDPVSCAFV 0.002 140GETVGGDEIV 0.002 134 GEQRDPGETV 0.002 118 QALRAKPKVY 0.002 212RMAEAELVQE 0.001 11 KYDMSGARLA 0.001 121 RAKPKVYIIQ 0.001 104 KLENLFEALN0.001 39 LEHMFRQLRF 0.001 13 DMSGARLALI 0.001 32 SEEDLDALEH 0.001 56PTAEQFQEEL 0.001 25 VTKAREGSEE 0.001 200 GHILELLTEV 0.001 207 TEVTRRMAEA0.001 77 DPVSCAFVVL 0.001 110 EALNNKNCQA 0.001 12 YDMSGARLAL 0.001 107NLFEALNNKN 0.001 113 NNKNCQALRA 0.001 123 KPKVYIIQAC 0.001 179RHDQKGSCFI 0.001 129 IQACRGEQRD 0.001 v.2-A11-10 mers: 213P1F11 34DTSPTDMIRK 0.600 40 MIRKAHALSR 0.160 33 QDTSPTDMIR 0.008 43 KAHALSRPWW0.006 9 GPTPFQDPLY 0.006 6 TVEGPTPFQD 0.006 32 SQDTSPTDMI 0.006 48SRPWWMCSPR 0.004 47 LSRPWWMCSR 0.004 2 HVYSTVEGPT 0.004 10 PTPFQDPLYL0.002 52 WMCSRRGKDI 0.002 5 STVEGPTPFQ 0.002 56 RRGKDISWNF 0.001 37PTDMIRKAHA 0.001 36 SPTDMIRKAH 0.001 46 ALSRPWWMCS 0.001 11 TPFQDPLYLP0.001 13 FQDPLYLPSE 0.001 45 HALSRPWWMC 0.001 17 LYLPSEAPPN 0.001 21SEAPPNPPLW 0.001 50 PWWMCSRRGK 0.000 23 APPNPPLWNS 0.000 54 CSRRGKDISW0.000 38 TDMIRKAHAL 0.000 18 YLPSEAPPNP 0.000 3 VYSTVEGPTP 0.000 44AHALSRPWWM 0.000 4 YSTVEGPTPF 0.000 26 NPPLWNSQDT 0.000 14 QDPLYLPSEA0.000 31 NSQDTSPTDM 0.000 19 LPSEAPPNPP 0.000 53 MCSRRGKDIS 0.000 39DMIRKAHALS 0.000 49 RPWWMCSRRG 0.000 22 EAPPNPPLWN 0.000 15 DPLYLPSEAP0.000 16 PLYLPSEAPP 0.000 28 PLWNSQDTSP 0.000 42 RKAHALSRPW 0.000 8EGPTPFQDPL 0.000 7 VEGPTPFQDP 0.000 12 PFQDPLYLPS 0.000 30 WNSQDTSPTD0.000 51 WWMCSRRGKD 0.000 1 LHVYSTVEGP 0.000 27 PPLWNSQDTS 0.000 41IRKAHALSRP 0.000 24 PPNPPLWNSQ 0.000 29 LWNSQDTSPT 0.000 55 SRRGKDISWN0.000 35 TSPTDMIRKA 0.000 20 PSEAPPNPPL 0.000 25 PNPPLWNSQD 0.000v.3-A11-10 mers: 213P1F11 9 GATLPSPFPY 0.018 10 ATLPSPFPYL 0.015 12LPSPFPYLSL 0.004 3 IIQACRGATL 0.004 11 TLPSPFPYLS 0.001 1 VYIIQACRGA0.001 4 IQACRGATLP 0.001 2 UOOQACRGAT 0.001 5 QACRGATLPS 0.000 6ACRGATLPSP 0.000 7 CRGATLPSPF 0.000 8 RGATLPSPFP 0.000 v.4-A11-10 mers:213P1F11 41 AFRGSSVHQK 0.200 13 VQPEKRTGLR 0.120 81 SETSASEEEK 0.060 69IVGRDLSISF 0.040 31 TFRLKEEQGR 0.040 12 SVQPEKRTGL 0.020 9 KSLSVQPEKR0.018 26 GECGQTFRLK 0.018 63 GGGVGDIVGR 0.012 60 EVFGGGVGDI 0.012 4CQEYDKSLSV 0.012 65 GVGDIVGRDL 0.006 8 DKSLSVQPEK 0.006 84 SASEEEKYDM0.004 47 VHQKLVNDPR 0.004 34 LKEEQGRAFR 0.004 70 VGRDLSISFR 0.004 82ETSASEEEKY 0.003 57 ETQEVFGGGV 0.003 18 RTGLRDENGE 0.003 24 ENGECGQTFR0.002 30 QTFRLKEEQG 0.002 46 SVHQKLVNDP 0.002 51 LVNDPRETQE 0.002 61VFGGGVGDIV 0.002 67 GDIVGRDLSI 0.002 50 KLVNDPRETQ 0.002 29 GQTFRLKEEQ0.002 20 GLRDENGECG 0.001 40 RAFRGSSVHQ 0.001 33 RLKEEQGRAF 0.001 39GRAFRGSSVH 0.001 3 KCQEYDKSLS 0.001 25 NGECGQTFRL 0.001 58 TQEVFGGGVG0.001 48 HQKLVNDPRE 0.001 35 KEEQGRAFRG 0.001 76 ISFRNSETSA 0.000 52VNDPRETQEV 0.000 75 SISFRNSETS 0.000 14 QPEKRTGLRD 0.000 32 FRLKEEQGRA0.000 43 RGSSVHQKLV 0.000 2 GKCQEYDKSL 0.000 77 SFRNSETSAS 0.000 10SLSVQPEKRT 0.000 42 FRGSSVHQKL 0.000 53 NDPRETQEVF 0.000 38 QGRAFRGSSV0.000 71 GRDLSISFRN 0.000 56 RETQEVFGGG 0.000 68 DIVGRDLSIS 0.000 23DENGECGQTF 0.000 37 EQGRAFRGSS 0.000 79 RNSETSASEE 0.000 44 GSSVHQKLVN0.000 6 EYDKSLSVQP 0.000 73 DLSISFRNSE 0.000 5 QEYDKSLSVQ 0.000 86SEEEKYDMSG 0.000 27 ECGQTFRLKE 0.000 64 GGVGDIVGRD 0.000 59 QEVFGGGVGD0.000 17 KRTGLRDENG 0.000 22 RDENGECGQT 0.000 54 DPRETQEVFG 0.000 62FGGGVGDIVG 0.000 45 SSVHQKLVND 0.000 19 TGLRDENGEC 0.000 74 LSISFRNSET0.000 80 NSETSASEEE 0.000 1 MGKCQEYDKS 0.000 21 LRDENGECGQ 0.000 85ASEEEKYDMS 0.000 66 VGDIVGRDLS 0.000 7 YDKSLSVQPE 0.000 78 FRNSETSASE0.000 83 TSASEEEKYD 0.000 28 CGQTFRLKEE 0.000 72 RDLSISFRNS 0.000 55PRETQEVFGG 0.000 16 EKRTGLRDEN 0.000 11 LSVQPEKRTG 0.000 49 QKLVNDPRET0.000 36 EEQGRAFRGS 0.000 15 PEKRTGLRDE 0.000 v.5-A11-10 mers: 213P1F114 RLALILRVTK 1.200 6 ALILRVTKAR 0.060 2 GARLALILRV 0.012 1 SGARLALILR0.008 10 RVTKAREGSE 0.006 5 LALILRVTKA 0.003 7 LILRVTKARE 0.001 8ILRVTKAREG 0.001 9 LRVTKAREGS 0.000 3 ARLALILRVT 0.000 v.6-A11-10 mers:213P1F11 4 ENLFEAMNNK 0.018 10 MNNKNCQALR 0.008 9 AMNNKNCQAL 0.004 2KLENLFEAMN 0.001 8 EAMNNKNCQA 0.001 5 NLFEAMNNKN 0.001 1 VKLENLFEAM0.000 3 LENLFEAMNN 0.000 6 LFEAMNNKNC 0.000 7 FEAMNNKNCQ 0.000

[0763] TABLE XIII Pos 123456789 Score SeqID v.1-A24-9 mers: 213P1F11 11KYDMSGARL 400.000 168 VYSTVEGYI 70.000 60 QFQEELEKF 19.800 104 KLENLFEAL17.280 227 TNPEIQSTL 10.080 183 KGSCFIQTL 9.600 112 LNNKNCQAL 7.200 31GSEEDLDAL 7.200 38 ALEHMFRQL 7.200 57 TAEQFQEEL 6.600 233 STLRKRLYL6.000 158 TIPTYTDAL 6.000 161 TYTDALHVY 6.000 177 AYRHDQKGS 5.000 194VFTKRKGHI 5.000 15 SGARLALIL 4.800 231 IQSTLRKRL 4.800 101 EMVKLENLF4.320 87 MAHGREGFL 4.000 195 FTKRKGHIL 4.000 13 DMSGARLAL 4.000 187FIQTLVDVF 3.600 35 DLDALEHMF 2.400 121 RAKPKVYII 2.400 223 KARKTNPEI2.200 86 LMAHGREGF 2.000 64 ELEKFQQAI 1.800 144 GGDEIVMVI 1.680 44RQLRFESTM 1.500 151 VILKDSPQTI 1.440 108 LFEALNNKN 1.188 198 RKGHILELL1.120 14 MSGARLALI 1.000 6 SLEEEKYDM 0.900 197 KRKGHILEL 0.880 205LLTEVTRRM 0.840 126 VYIIQACRG 0.750 174 GYIAYRHDQ 0.750 186 CFIQTLVDV0.750 75 REDPVSCAF 0.672 42 MFRQLRFES 0.660 100 GEMVKLENL 0.600 28AREGSEEDL 0.600 94 FLKGEDGEM 0.550 79 VSCAFVVLM 0.500 142 TVGGDEIVM0.500 78 PVSCAFVVL 0.480 53 KRDPTAEQF 0.480 97 GEDGEMVKL 0.440 210TRRMAEAEL 0.440 226 KTHPEIQST 0.432 179 RHDQKGSCF 0.400 40 EHMFRQLRF0.300 18 RLALILCVT 0.280 199 KGHILELLT 0.240 201 HILELLTEV 0.238 99DGEMVKLEM 0.231 155 SPQTIPTYT 0.210 147 EIVMVIKDS 0.210 164 DALHVYSTV0.210 123 KPKVYIIQA 0.200 157 QTIPTYTDA 0.180 202 ILELLTEVT 0.180 170STVEGYIAY 0.180 20 ALILCVTKA 0.165 219 VQEGKARKT 0.165 118 QALRAKPKV0.165 50 STMKRDPTA 0.150 150 MVIKDSPQT 0.150 47 RFESTMKRD 0.150 154DSPQTIPTY 0.150 206 LTEVTRRMA 0.150 106 ENLFEALNN 0.150 111 ALNNKNCQA0.150 67 KFQQAIDSR 0.150 141 ETVGGDEIV 0.150 77 DPVSCAFVV 0.150 180HDQKGSCFI 0.150 80 SCAFVXTLMA 0.140 188 TQTLVDVFT 0.140 184 GSCFIQTLV0.140 30 EGSEEDLDA 0.120 143 VGGDEIVMV 0.120 162 YTDALHVYS 0.120 73DSREDPVSC 0.120 135 EQRDPGETV 0.120 208 EVTRRMAEA 0.110 140 GETVGGDEI0.110 232 QSTLRKRLY 0.100 16 GARLALILC 0.100 119 ALRAKPKVY 0.100 167HVYSTVEGY 0.100 24 CVTKAREGS 0.100 49 ESTMKRDPT 0.100 71 AIDSREDPV 0.100120 LRAKPKVYI 0.100 169 YSTVEGYIA 0.100 34 EDLDALEHM 0.090 82 AFVVLMAHG0.090 93 GFLKGEDGE 0.075 v.2-A24-9 mers: 213P1F11 2 VYSTVEGPT 7.000 56RGKDISWNF 6.720 38 DMIRKAHAL 6.000 8 GPTPFQDPL 4.800 10 TPFQDPLYL 4.0004 STVEGPTPF 3.600 52 MCSRRGKDI 1.000 16 LYLPSEAPP 0.900 44 HALSRPWWM0.750 31 SQDTSPTDM 0.500 20 SEAPPNPPL 0.480 42 KAHALSRPW 0.240 14DPLYLPSEA 0.198 21 EAPPNPPLW 0.180 22 APPNPPLWN 0.150 17 YLPSEAPPN 0.15012 FQDPLYLPS 0.150 35 SPTDMIRKA 0.132 46 LSRPWWMCS 0.120 45 ALSRPWWMC0.100 29 WNSQDTSPT 0.100 32 QDTSPTDMI 0.100 53 CSRRGKDIS 0.100 7EGPTPFQDP 0.022 48 RPWWMCSRR 0.020 55 RRGKDISWN 0.020 26 PPLWNSQDT 0.01823 PPNPPLWNS 0.018 30 NSQDTSPTD 0.018 9 PTPFQDPLY 0.015 50 WWMCSRRGK0.015 25 NPPLWNSQD 0.015 34 TSPTDMIRK 0.015 28 LWNSQDTSD 0.015 37TDNIRKAHA 0.015 5 TVEGPTPFQ 0.015 18 LPSEAPPNP 0.012 33 DTSPTDMIR 0.01251 WMCSRRGKD 0.011 54 SRRGKDISW 0.010 43 AHALSRPWW 0.010 27 PLWNSQDTS0.010 3 YSTVEGPTP 0.010 1 HVYSTVEGP 0.010 11 PFQDPLYLP 0.009 24PNPPLWNSQ 0.003 41 RKAHALSRP 0.002 19 PSEAPPNPP 0.002 47 SRPWWMCSR 0.00213 QDPLYLPSE 0.002 36 PTDMIRKAH 0.001 6 VEGPTPFQD 0.001 40 IRKAHALSR0.001 49 PWWMCSRRG 0.001 15 PLYLPSEAP 0.001 v.3-A24-9 mers: 213P1F11 10TLPSPFPYL 7.200 7 RGATLPSPF 4.800 3 IQACRGATL 4.000 12 PSPFPYLSL 0.600 9ATLPSPFPY 0.180 2 IIQACRGAT 0.150 1 YIIQACRGA 0.150 11 LPSPFPYLS 0.120 5ACRGATLPS 0.100 4 QACRGATLP 0.010 8 GATLPSPFP 0.010 6 CRGATLPSP 0.001v.4-A24-9 mers: 213P1F11 43 RGSSVHQKL 14.784 3 KCQEYDKSL 14.400 13VQPEKRTGL 7.200 66 VGDIVGRDL 5.600 61 VFGGGVGDI 5.000 24 ENGECGQTF 2.88070 VGRDLSISF 2.880 54 DPRETQEVF 2.400 68 DIVGRDLSI 1.500 85 ASEEEKYDM0.900 77 SFRNSETSA 0.500 6 EYDKSLSVQ 0.500 26 GECGQTFRL 0.400 34LKEEQGRAF 0.360 50 KLVNDPRET 0.330 33 RLKEEQGRA 0.240 4 CQEYDKSLS 0.15011 LSVQPEKRT 0.150 58 TQEVFGGGV 0.150 45 SSVHQKLVN 0.150 62 FGGGVGDIV0.140 20 GLRDENGEC 0.132 37 EQGRAFRGS 0.120 73 DLSISFRNS 0.120 83TSASEEEKY 0.110 75 SISFRNSET 0.110 44 GSSVHQKLV 0.100 38 QGRAFRGSS 0.10069 IVGRDLSIS 0.100 76 ISFRNSETS 0.100 41 AFRGSSVHQ 0.050 31 TFRLKEEQG0.050 9 KSLSVQPEK 0.046 72 RDLSISFRN 0.042 57 ETQEVFGGG 0.030 17KRTGLRDEN 0.026 79 RNSETSASE 0.024 40 RAFRGSSVH 0.020 18 RTGLRDENG 0.02053 NDPRETQEV 0.020 86 SEEEKYDMS 0.018 12 SVQPEKRTG 0.018 74 LSISFRNSE0.018 51 LVNDPRETQ 0.018 19 TGLRDENGE 0.018 65 GVGDIVGRD 0.017 28CGQTFRLKE 0.017 80 NSETSASEE 0.017 23 DENGECGQT 0.015 25 NGECGQTFR 0.01564 GGVGDIVGR 0.015 67 GDIVGRDLS 0.015 78 FRNSETSAS 0.015 14 QPEKRTGLR0.015 48 HQKLVNDPR 0.014 30 QTFRLKEEQ 0.013 5 QEYDKSLSV 0.012 52VNDPRETQE 0.012 27 ECGQTFRLK 0.012 84 SASEEEKYD 0.012 2 GKCQEYDKS 0.01110 SLSVQPEKR 0.011 29 GQTFRLKEE 0.011 82 ETSASEEEK 0.011 39 GRAFRGSSV0.010 46 SVGQKLVND 0.010 60 EVFGGGVGD 0.010 63 GGGVGDIVG 0.010 1MGKCQEYDE 0.010 35 KEEQGRAFR 0.003 22 RDENGECGQ 0.003 47 VHQKLVNDP 0.00256 RETQEVFGG 0.002 32 FRLKEEQGR 0.002 59 QEVFGGGVG 0.002 36 EEQGRAFRG0.002 49 QKLVNDPRE 0.002 8 DKSLSVQPE 0.001 7 YDKSLSVQP 0.001 21LRDENGECG 0.001 81 SETSASEEE 0.001 42 FRGSSVHQK 0.001 16 EKRTGLRDE 0.00171 GRDLSISFR 0.001 55 PRETQEVPG 0.000 15 PEKRTGLRD 0.000 v.5-A24-9 mers:213P1F11 3 RLALILRVT 0.280 9 RVTKAREGS 0.200 5 ALILRVTKA 0.165 6LILRVTKAR 0.021 2 ARLALILRV 0.018 4 LALILRVTK 0.018 1 GARLALILR 0.010 7ILRVTKARE 0.010 8 LRVTKAREG 0.002 v.6-A24-9 mers: 213P1F11 9 MNNKNCQAL7.200 1 KLENLFEAM 2.160 5 LFEAMNNKN 0.990 3 ENLFEAMNN 0.150 8 AMNNKNCQA0.150 7 EAMNNKNCQ 0.018 2 LENLFEAMN 0.015 4 NLFEAMNNK 0.014 6 FEAMNNKNC0.010

[0764] TABLE XIV Pos 1234567890 Score SeqID v.1-A24-10 mers: 213P1F11226 KTNPEIQSTL 20.160 194 VFTKRKGHIL 20.000 186 CFIQTLVDVF 18.000 96KGEDGEMVKL 15.840 11 KYDMSGARLA 10.000 27 KAREGSEEDL 9.600 37 DALEHMFRQL8.640 161 TYTDALHVYS 7.200 111 ALNNKNCQAL 7.200 230 EIQSTLRKRL 7.200 77DPVSCAFVVL 7.200 157 QTIPTYTDAL 7.200 99 DGEMVKLENL 6.000 177 AYRHDQKGSC5.000 168 VYSTVEGYIA 5.000 14 MSGARLALIL 4.800 30 EGSEEDLDAL 4.800 209VTRRMAEAEL 4.400 93 GFLKGEDGEM 4.125 232 QSTLRKRLYL 4.000 86 LMAHGREGFL4.000 85 VLMAHGREGF 3.000 59 EQFQEELEKF 2.200 150 MVIKDSPQTI 1.800 5RSLEEEKYDM 1.800 143 VGGDEIVMVI 1.680 167 HVYSTVECYI 1.400 197KRKGHILELL 1.120 204 ELLTEVTRRM 1.050 103 VKLENLFEAL 1.037 119ALRAKPKVYI 1.000 193 DVFTKRKGHI 1.000 13 DMSGARLALI 1.000 141 ETVGGDEIVM0.750 108 LFEALNNKNC 0.750 126 VYIIQACRCE 0.750 174 GYIAYRHDQK 0.750 12YDMSGARLAL 0.600 42 MFRQLRFEST 0.600 56 PTAEQFQEEL 0.528 74 SREDPVSCAF0.504 10 EKYDMSGARL 0.480 182 QKGSCFIQTL 0.480 196 TKRKGHILEL 0.440 100GEMVKLENLF 0.432 34 EDLDALEHMF 0.432 123 KPKVYIIQAC 0.336 133 RGEQRDPGET0.330 104 KLENLFEALN 0.300 183 KGSCFIQTLV 0.280 52 MKRDPTAEQF 0.240 178YRHDQKGSCF 0.240 63 EELEKFQQAI 0.216 201 HILELLTEVT 0.216 67 KFQQAIDSRE0.210 187 FIQTLVDVFT 0.210 154 DSPQTIPTYT 0.210 179 RHDQKGSCFI 0.200 39LEHMFRQLRF 0.200 218 LVQEGKARKT 0.198 107 NLFEALNNKN 0.190 6 SLEEEKYDMS0.180 70 QAIDSREDPV 0.180 139 PGETVGGDEI 0.165 19 LALILCVTKA 0.165 215EAELVQEGKA 0.165 47 RFESTMKRDP 0.150 23 LCVTKAREGS 0.150 118 QALRAKPKVY0.150 149 VMVIKDSPQT 0.150 110 EALNNKNCQA 0.150 219 VQEGKARKTN 0.150 79VSCAFVVLMA 0.140 41 HMFRQLRFES 0.132 73 DSREDPVSCA 0.120 181 DQKGSCFIQT0.120 205 LLTEVTRRMA 0.120 16 GARLALILCV 0.120 102 MVKLENLFEA 0.110 3NPRSLEEEKY 0.110 222 GKARKTNPEI 0.110 117 CQALRAKPKV 0.110 60 QFQEELEKFQ0.108 169 YSTVEOYIAY 0.100 176 IAYRHDQKGS 0.100 185 SCFIQTLVDV 0.100 120LRAKPKVYII 0.100 231 IQSTLRKRLY 0.100 113 NNKNCQALRA 0.100 142TVGGDEIVMV 0.100 94 FLKGEDGEMV 0.100 49 ESTMKRDPTA 0.100 15 SGARLALILC0.100 162 YTDAILHVYST 0.100 71 AIDSREDPVS 0.100 159 IPTYTDALHV 0.100 82AFVVLMAHGR 0.075 43 FRQLRFESTM 0.075 78 PVSCAFVVLM 0.050 33 EEDLDALEHM0.050 v.2-A24-10 mers: 213P1F11 17 LYLPSEAPPN 9.000 8 EGPTPFQDPL 6.000 4YSTVEGPTPF 2.000 32 SQDTSPTDMI 1.000 52 WMCSRRGKDI 1.000 31 NSQDTSPTDM0.900 20 PSEAPPNPPL 0.600 10 PTPFQDPLYL 0.600 38 TDMIRKAHAL 0.600 56RRGKDISWNF 0.560 3 VYSTVEGPTP 0.500 43 KAHALSRPWW 0.200 26 NPPLWNSQDT0.180 22 EAPPNPPLWN 0.180 35 TSPTDMIRKA 0.165 29 LWNSQDTSPT 0.150 23APPNPPLWNS 0.150 39 DMIRKAHALS 0.150 45 HALSRPWWMC 0.150 2 HVYSTVEGPT0.140 9 GPTPFQDPLY 0.120 12 PFQDPLYLPS 0.108 46 ALSRPWWMCS 0.100 53MCSRRGKDIS 0.100 54 CSRRGKDISW 0.100 44 AHALSRPWWM 0.050 42 RKAHALSRPW0.024 49 RPWWMCSRRG 0.020 14 QDPLYLPSEA 0.020 5 STVEGPTPFQ 0.018 36SPTDMIRKAH 0.017 51 WWMCSRRGKD 0.017 18 YLPSEAPPNP 0.015 6 TVEGPTPFQD0.015 27 PPLWNSQDTS 0.015 15 DPLYLPSEAP 0.015 19 LPSEAPPNPP 0.014 13FQDPLYLPSE 0.012 21 SEAPPNRPLW 0.012 34 DTSPTDMIRK 0.012 47 LSRPWWMCSR0.012 55 SRRGKDISWN 0.010 37 PTDMIRKAHA 0.010 11 TPFQDPLYLP 0.010 30WNSQDTSPTD 0.010 40 MTRKAHALSR 0.010 24 PPNPPLWNSQ 0.003 25 PNPPLWNSQD0.002 7 VEGPTPFQDP 0.002 48 SRPWWMCSRR 0.002 1 LHVYSTVEGP 0.002 50PWWMCSRRGK 0.001 28 PLWNSQDTSP 0.001 33 QDTSPTDMIR 0.001 41 IRKAHALSRP0.001 16 PLYLPSEAPP 0.001 v.3-A24-10 mers: 213P1F11 10 ATLPSPFPYL 8.6401 VYIIQACRGA 7.500 3 IIQACRGATL 6.000 12 LPSPFPYLSL 4.800 7 CRGATLPSPF0.240 11 TLPSPFPYLS 0.150 2 YIIQACRGAT 0.150 5 QACRGATLPS 0.100 9GATLPSPFPY 0.100 8 RGATLPSPFP 0.020 4 IQACRGATLP 0.010 6 ACRGATLPSP0.010 v.4-A24-10 mers: 213P1F11 12 SVQPEKRTGL 7.200 65 GVGDIVGRDL 6.72025 NGECGQTFRL 6.000 33 RLKEEQGRAF 4.800 69 IVGRDLSISF 2.400 60EVFGGGVGDI 1.000 42 FRGSSVHQKL 0.739 61 VFGGGVGDIV 0.700 84 SASEEEKYDM0.600 6 EYDKSLSVQP 0.600 77 SFRNSETSAS 0.500 2 GKCQEYDKSL 0.400 23DENGECGQTF 0.360 3 KCQEYDKSLS 0.360 53 NDPRETQEVF 0.300 43 RGSSVHQKLV0.200 85 ASEEEKYDMS 0.180 57 ETQEVFGGGV 0.180 74 LSISFRNSET 0.165 19TGLRDENGEC 0.165 52 VNDPRETQEV 0.158 68 DIVGRDLSIS 0.150 67 GDIVGRDLSI0.150 4 CQEYDKSLSV 0.150 82 ETSASEEEKY 0.110 1 MGKCQEYDKS 0.110 38QGRAFRGSSV 0.100 44 GSSVHQKLVN 0.100 37 EQGRAFRGSS 0.100 76 ISFRNSETSA0.100 10 SLSVQPEKRT 0.100 66 VGDIVGRDLS 0.100 75 SISFRNSETS 0.100 31TFRLKEEQGR 0.060 41 AFRGSSVHQK 0.050 72 RDLSISFRNS 0.036 9 KSLSVQPEKR0.033 22 RDENGECGQT 0.030 50 KLVNDPRETQ 0.030 79 RNSETSASEE 0.026 18RTGLRDENGE 0.024 64 GGVGDIVGRD 0.021 40 RAFRGSSVHQ 0.020 36 EEQGRAFRGS0.018 13 VQPEKRTGLR 0.018 51 LVNDPRETQE 0.018 28 CGQTFRLKEE 0.017 80NSETSASEEE 0.017 49 QKLVNDPRET 0.017 58 TQEVFGGGVG 0.015 11 LSVQPEKRTG0.0 15 14 QPEKRTGLRD 0.015 32 FRLKEEQGRA 0.015 45 SSVHQKLVND 0.015 46SVHQKLVNDP 0.014 71 GRDLSISFRN 0.014 16 EKRTGLRDEN 0.013 29 GQTFRLKEEQ0.013 70 VGRDLSISFR 0.012 73 DLSISFRNSE 0.012 20 GLRDENGECG 0.012 54DPRETQEVFG 0.012 24 ENGECGQTFR 0.012 27 ECGQTFRLKE 0.011 30 QTFRLKEEQG0.010 83 TSASEEEKYD 0.010 63 GGGVGDIVGR 0.010 48 HQKLVNDPRE 0.010 62FGGGVGDIVG 0.010 56 RETQEVFGGG 0.003 35 KEEQGPAFRG 0.003 47 VHQKLVNDPR0.002 17 KRTGLRDENG 0.002 34 LKEEQGRAFR 0.002 86 SEEEKYDMSG 0.002 8DKSLSVQPEK 0.002 59 QEVFGGGVGD 0.002 78 FRNSETSASE 0.002 26 GECGQTFRLK0.001 7 YDKSLSVQPE 0.001 21 LRDENGECGQ 0.001 5 QEYDKSLSVQ 0.001 81SETSASEEEK 0.001 39 GRAFRGSSVH 0.001 55 PRETQEVFGG 0.000 15 PEKRTGLRDE0.000 v.5-A24-10 mers: 213P1F11 5 LALILRVTKA 0.165 2 GARLALILRV 0.120 4RLALILRVTK 0.024 3 ARLALILRVT 0.021 6 ALILRVTKAR 0.021 10 RVTKAREGSE0.020 7 LILRVTKARE 0.015 9 LRVTKAREGS 0.015 8 ILRVTKAREG 0.011 1SGARLALILR 0.010 v.6-A24-10 mers: 213P1F11 9 AMNNKNCQAL 7.200 6LFEAMNNKNC 0.750 2 KLENLFEAMN 0.300 5 NLFEAMNNKN 0.158 8 EANNNKNCQA0.150 1 VKLENLFEAM 0.130 4 ENLFEANNNK 0.018 3 LENLFEAMNN 0.015 10MNNKNCQALR 0.015 7 FEAMNNKNCQ 0.001

[0765] TABLE XV Pos 123456789 Score SeqID v.1-B7-9 mers: 213P1F11 87MAHGREGFL 12.000 223 KARKTNPEI 12.000 13 DMSGARLAL 6.000 233 STLRKRLYL6.000 231 IQSTLRKRL 6.000 142 TVGGDEIVM 5.000 112 LNNKNCQAL 4.000 227TNPEIQSTL 4.000 210 TRRMAEAEL 4.000 183 KGSCFTQTL 4.000 77 DPVSCAFVV4.000 158 TIPTYTDAL 4.000 15 SGARLALIL 4.000 195 FTKRKGHIL 4.000 57TAEQFQEEL 3.600 38 ALEHMFRQL 3.600 16 GARLALILC 3.000 135 EQRDPGETV3.000 3 NPRSLEEEK 2.000 155 SPQTIPTYT 2.000 78 PVSCAFVVL 2.000 123KPKVYIIQA 2.000 31 GSEEDLDAL 1.200 121 RAKPKVYII 1.200 100 GEMVKLENL1.200 104 KLENLFEAL 1.200 94 FLKGEDGEM 1.000 73 DSREDPVSC 1.000 79VSCAFVVLM 1.000 44 RQLRFESTM 1.000 205 LLTEVTRRM 1.000 118 QALRAKPKV0.600 164 DALHVYSTV 0.600 119 ALRAKPKVY 0.600 208 EVTRRMAEA 0.500 150MVIKDSPQT 0.500 197 KRKGHILEL 0.400 198 RKGHILELL 0.400 14 MSGARLALI0.400 151 VIKDSPQTI 0.400 28 AREGSEEDL 0.360 131 ACRGEQRDP 0.300 27KAREGSEED 0.300 111 ALNNKNCQA 0.300 20 ALILCVTKA 0.300 6 SLEEEKYDM 0.30050 STMKRDPTA 0.300 55 DPTAEQFQE 0.200 184 GSCFTQTLV 0.200 159 IPTYTDALH0.200 143 VGGDEIVMV 0.200 201 HILELLTEV 0.200 138 DPGETVGGD 0.200 141ETVGGDEIV 0.200 71 AIDSREDPV 0.180 24 CVTKAREGS 0.150 148 IVMVIKDSP0.150 49 ESTMKRDPT 0.150 97 GEDGEMVKL 0.120 144 GGDEIVMVI 0.120 11KYDMSGARL 0.120 64 ELEKFQQAI 0.120 199 KGHILELLT 0.100 80 SCAFVVLMA0.100 34 EDLDALEHM 0.100 89 HGREGFLKG 0.100 234 TLRKRLYLQ 0.100 45QLRFESTMK 0.100 188 IQTLVDVFT 0.100 167 HVYSTVEGY 0.100 18 RLALILCVT0.100 226 KTNPEIQST 0.100 209 VTRRMAEAE 0.100 157 QTIPTYTDA 0.100 169YSTVEGYIA 0.100 30 EGSEEDLDA 0.100 193 DVFTKRKGH 0.075 177 AYRHDQKGS0.060 120 LRAKPKVYI 0.060 211 RRMAEAELV 0.060 17 ARLALILCV 0.060 228NPEIQSTLR 0.060 218 LVQEGKARK 0.050 125 KVYIIQACR 0.050 102 MVKLENLFE0.050 84 VVLMAHGRE 0.050 83 FVVLMAHGR 0.050 70 QAIDSREDP 0.045 206LTEVTRRMA 0.045 140 GETVGGDEI 0.040 168 VYSTVEGYI 0.040 194 VFTKRKGHI0.040 180 HDQKGSCFI 0.040 86 LMAHGREGF 0.030 19 LALILCVTK 0.030 37DALEHMFRQ 0.030 12 YDMSGARLA 0.030 165 ALHVYSTVE 0.030 85 VLMAHGREG0.030 216 AELVQEGKA 0.030 v.2-B7-9 mers 8 GPTPFQDPL 80.000 10 TPFQDPLYL80.000 38 DMIRKAHAL 4.000 44 HALSRPWWM 3.000 14 DPLYLPSEA 2.000 35SPTDMIRKA 2.000 22 APPNPPLWN 1.800 20 SEAPPNPPL 0.600 45 ALSRPWWMC 0.45052 MCSRRGKDI 0.400 31 SQDTSPTDM 0.300 48 RPWWMCSRR 0.200 46 LSRPWWMCS0.200 53 SCRRGKDIS 0.200 39 MIRKAHALS 0.200 25 NPPLWNSQD 0.200 26PPLWNSQDT 0.200 18 LPSEAPPNP 0.200 29 WNSQDTSPT 0.100 42 KAHALSRPW 0.06032 QDTSPTDMI 0.060 23 PPNPPLWNS 0.060 21 EAPPNPPLW 0.060 1 HVYSTVEGP0.050 37 TDMIRKAHA 0.030 5 TVEGPTPFQ 0.023 54 SRRGKDISW 0.020 56RGKDISWNF 0.020 4 STVEGPTPF 0.020 17 YLPSEAPPN 0.020 7 EGPTPFQDP 0.01551 WMCSRRGKD 0.015 33 DTSPTDMIR 0.010 2 VYSTVEGPT 0.010 34 TSPTDMIRK0.010 30 NSQDTSPTD 0.010 3 YSTVEGPTP 0.010 43 AHALSRPWW 0.009 12FQDPLYLPS 0.006 50 WWMCSRRGK 0.005 9 PTPFQDPLY 0.002 55 RRGKDISWN 0.00227 PLWNSQDTS 0.002 15 PLYLPSEAP 0.002 41 RKAHALSRP 0.001 6 VEGPTPFQD0.001 13 QDPLYLPSE 0.001 40 IRKAHALSR 0.001 47 SRPWWMCSR 0.001 24PNPPLWNSQ 0.001 16 LYLPSEAPP 0.001 28 LWNSQDTSP 0.001 19 PSEAPPNPP 0.00036 PTDMIRKAH 0.000 11 PFQDPLYLP 0.000 49 PWWMCSRRG 0.000 v.3-B7-9 mers:213P1F11 10 TLPSPFPYL 6.000 3 IQACRGATL 4.000 5 ACRGATLPS 0.600 12PSPFPYLSL 0.600 11 LPSPFPYLS 0.400 2 IIQACRGAT 0.150 1 YIIQACRGA 0.100 9ATLPSPFPY 0.060 8 GATLPSPFP 0.045 4 QACRGATLF 0.030 7 RGATLPSPF 0.020 6CRGATLPSP 0.001 v.4-B7-9 mers: 213P1F11 13 VQPEKRTGL 6.000 3 KCQEYDKSL4.000 54 DPRETQEVF 4.000 43 RGSSVHQKL 4.000 66 VGDIVGRDL 1.200 20GLRDENGEC 1.000 85 ASEEEKYDM 0.900 26 GECGQTFRL 0.400 68 DIVGRDLSI 0.40038 QGRAFRGSS 0.300 62 FGGGVGDIV 0.200 70 VGRDLSISF 0.200 44 GSSVHQKLV0.200 11 LSVQPEKRT 0.150 51 LVNDPRETQ 0.113 77 SFRNSETSA 0.100 69IVGRDLSIS 0.100 75 SISFRNSET 0.100 33 RLKEEQGRA 0.100 50 KLVNDPRET 0.10014 QPEKRTGLR 0.060 58 TQEVFGGGV 0.060 60 EVFGGGVGD 0.050 12 SVQPEKRTG0.050 46 SVHQKLVND 0.050 65 GVGDIVGRD 0.050 61 VFGGGVGDI 0.040 84SASEEEKYD 0.030 41 AFRGSSVHQ 0.030 40 RAFRGSSVH 0.030 83 TSASEEEKY 0.02037 EQGRAFRGS 0.020 73 DLSISFRNS 0.020 24 ENGECGQTF 0.020 39 GRAFRGSSV0.020 53 NDPRETQEV 0.020 5 QEYDKSLSV 0.020 45 SSVHQKLVN 0.020 76ISFRNSETS 0.020 74 LSISFRNSE 0.015 28 CGQTRFLKE 0.015 27 ECGQTFRLK 0.0109 KSLSVQPEK 0.010 23 DENGECGQT 0.010 30 QTFRLKEEQ 0.010 10 SLSVQPEKR0.010 1 MGKCQEYDK 0.010 63 GGGVGDIVG 0.010 82 ETSASEEEK 0.010 57ETQEVFGGG 0.010 64 GGVGDIVGR 0.010 18 RTGLRDENG 0.010 16 EKRTGLRDE 0.01048 HQKLVNDPR 0.010 29 GQTFRLKEE 0.010 79 RNSETSASE 0.010 19 TGLRDENGE0.010 31 TFRLKEEQG 0.010 4 CGEYDKSLS 0.006 67 GDIVGRDLS 0.003 17KRTGLRDEN 0.003 52 VNDPRETQE 0.003 25 NGECGQTFR 0.003 80 NSETSASEE 0.0032 GKCQEYDKS 0.002 72 RDLSISFRN 0.002 78 FRNSETSAS 0.002 59 QEVFGGGVG0.001 47 VHQKLVNDP 0.001 42 FRGSSVHQK 0.001 81 SETSASEEE 0.001 49QKLVNDPRE 0.001 36 EEQGRAFRG 0.001 8 DKSLSVQPE 0.001 32 FRLKEEQGR 0.0017 YDKSLSVQP 0.001 56 RETQEVFGG 0.001 34 LKEEQGRAF 0.001 86 SEEEKYDMS0.001 35 KEEQGRAFR 0.000 6 EYDKSLSVQ 0.000 21 LRDENGECG 0.000 71GRDLSISFR 0.000 22 RDENGECGQ 0.000 15 PEKRTGLRD 0.000 55 PRETQEVFG 0.000v.5-B7-9 mers: 213P1F11 1 GARLALILR 0.300 5 ALILRVTKA 0.300 9 RVTKAREGS0.150 7 ILRVTKARE 0.100 3 RLALILRVT 0.100 2 ARLALILRV 0.060 4 LALILRVTK0.045 6 LILRVTKAR 0.010 8 LRVTKAREG 0.001 v.6-B7-9 mers: 213P1F11 9MNNKNCQAL 4.000 8 AMNNKNCQA 0.300 1 KLENLFEAM 0.300 7 EAMNNKNCQ 0.090 3ENLFEAMNN 0.020 6 FEAMNNKNC 0.010 4 NLFEAMNNK 0.010 2 LENLFEAMN 0.002 5LFEAMNNKN 0.001

[0766] TABLE XVI Pos 1234567890 Score SeqID v.1-B7-10 mers:213P1F11 27KAREGSEEDL 120.000 77 DPVSCAFVVL 80.000 209 VTRRMAEAEL 40.000 119ALRAKPKVYI 18.000 111 ALNNKNCQAL 12.000 37 DALEHMFRQL 12.000 16GARLALILCV 6.000 232 QSTLRKRLYL 6.000 230 EIQSTLRKRL 6.000 157QTIPTYTDAL 4.000 3 NPRSLEEEKY 4.000 226 KTNPEIQSTL 4.000 196 TKRKGHILEL4.000 159 IPTYTDALHV 4.000 30 EGSEEDLDAL 4.000 14 MSGARLALIL 4.000 86LMAHGREGFL 4.000 193 DVFTKRKGHI 2.000 167 HVYSTVEGYT 2.000 150MVIKDSPQTI 2.000 123 KPKVYIIQAC 2.000 12 YDMSGARLAL 1.800 73 DSREDPVSCA1.500 96 KGEDGEMVKL 1.200 99 DGEMVKLENL 1.200 5 RSLEEEKYDM 1.000 204ELLTEVTRRM 1.000 142 TVGGDEIVMV 1.000 141 ETVGGDEIVM 1.000 70 QAIDSREDPV0.600 78 PVSCAFVVLM 0.500 102 MVKLENLFEA 0.500 218 LVQEGKARKT 0.500 131ACRGEQRDPG 0.450 10 EKYDMSGARL 0.400 13 DMSGARLALI 0.400 194 VFTKRKGHIL0.400 103 VKLENLFEAL 0.400 182 QKGSCFIQTL 0.400 143 VGGDEIVMVI 0.400 56PTAEQFQEEL 0.400 197 KRKGHILELL 0.400 223 KARKTNPEIQ 0.300 19 LALILCVTKA0.300 155 SPQTIPTYTD 0.300 177 AYRHDQKGSC 0.300 110 EALNNKNCQA 0.300 183KGSCFIQTLV 0.200 94 FLKGEDGEMV 0.200 185 SCFIQTLVDV 0.200 138 DPGETVGGDE0.200 55 DPTAEQFQEE 0.200 210 TRRMAEAELV 0.200 117 CQALRAKPKV 0.200 205LLTEVTRRMA 0.150 148 IVMVIKDSPQ 0.150 135 EQRDPCETVG 0.100 42 MFRQLRFEST0.100 79 VSCAFVVLMA 0.100 89 HGREGFLKGE 0.100 113 NNKNCQALRA 0.100 149VMVIKDSPQT 0.100 181 DQKGSCFIQT 0.100 93 GFLKGEDGEM 0.100 43 FRQLRFESTM0.100 15 SGARLALILC 0.100 45 QLRFESTMKR 0.100 187 FIQTLVDVFT 0.100 201HILELLTEVT 0.100 154 DSPQTIPTYT 0.100 49 ESTMKRDPTA 0.100 85 VLMAHGREGF0.090 215 EAELVQEGKA 0.090 228 NPEIQSTLRK 0.060 176 IAYRHDQKGS 0.060 118QALPAKPKVY 0.060 84 VVLMAHGREG 0.050 125 KVYIIQACRG 0.050 208 EVTRRMAEAE0.050 24 CVTKAREGSE 0.050 83 FVVLMAHGRE 0.050 63 EELEKFQQAI 0.040 120LRAKPKVYII 0.040 222 GKARKTNPEI 0.040 130 QACRGEQRDP 0.030 134GEQRDPGETV 0.030 23 LCVTKAREGS 0.030 165 ALHVYSTVEG 0.030 17 ARLALILCVT0.030 20 ALILCVTKAR 0.030 122 AKPKVYIIQA 0.030 81 CAFVVLMAHG 0.030 50STMKRDPTAE 0.030 164 DALHVYSTVE 0.030 41 HMFRQLRFES 0.030 87 MAHGREGFLK0.030 121 RAKPKVYIIQ 0.030 33 EEDLDALEHM 0.030 162 YTDALHVYST 0.030 133RGEQRDPGET 0.030 v.2-B7-10 mers: 213P1F11 8 EGPTPFQDPL 4.000 26NPPLWNSQDT 2.000 23 APPNPPLWNS 1.800 38 TDMIRKAHAL 1.200 31 NSQDTSPTDM1.000 2 HVYSTVEGPT 0.500 45 HALSRPWWMC 0.450 9 GPTPFQDPLY 0.400 52WMCSRRGKDI 0.400 10 PTPFQDPLYL 0.400 36 SPTDMIRKAH 0.300 15 DPLYLPSHAP0.300 11 TPFQDPLYLP 0.300 44 AHALSRPWWM 0.300 19 LPSEAPPNPP 0.300 49RPWWMCSRRG 0.200 54 CSRRGKDISW 0.200 32 SQDTSPTDMI 0.180 20 PSEAPPNPPL0.180 35 TSPTDMIRKA 0.100 40 MIRKAHALSR 0.100 47 LSRPWWMCSR 0.100 43KAHALSRPWW 0.090 22 EAPPNPPLWN 0.090 46 ALSRPWWMCS 0.060 27 PPLWNSQDTS0.040 4 YSTVEGPTPF 0.020 55 SRRGKDISWN 0.020 39 DMIRKAHALS 0.020 24PPNPPLWNSQ 0.020 53 MCSRRGKDIS 0.020 6 TVEGPTPFQD 0.015 5 STVEGPTPFQ0.015 30 WNSQDTSPTD 0.010 29 LWNSQDTSPT 0.010 18 YLPSEAPPNP 0.100 34DTSPTDMIRK 0.010 14 QDPLYLPSEA 0.010 51 WWMCSRRGKD 0.005 13 FQDPLYLPSE0.003 37 PTDMIRKAHA 0.003 56 RRGKDISWNF 0.002 42 RKAHALSRPW 0.002 21SEAPPNPPLW 0.002 17 LYLPSEAPPN 0.002 7 VEGPTPFQDP 0.002 48 SRPWWMCSRR0.001 25 PNPPLWNSQD 0.001 33 QDTSPTDMIR 0.001 41 IRKAHALSRP 0.001 3VYSTVEGPTP 0.001 16 PLYLPSEAPP 0.001 28 PLWNSQDTSP 0.001 1 LHVYSTVEGP0.001 12 PFQDPLYLPS 0.000 50 PWWMCSRRGK 0.000 v.3-B7-10 mers: 213P1F1112 LPSPFPYLSL 120.000 10 ATLPSPFPYL 18.000 3 IIQACRGATL 4.000 6ACRGATLPSP 0.300 2 YIIQACRGAT 0.150 9 GATLPSPFPY 0.060 5 QACRGATLPS0.060 11 TLPSPFPYLS 0.020 8 RGATLPSPFP 0.015 4 IQACRGATLP 0.010 1VYIIQACRGA 0.010 7 CRGATLPSPF 0.002 v.4-B7-10 mers: 213P1F11 12SVQPEKRTGL 30.000 65 GVGDIVGRDL 20.000 84 SASEEEKYDM 3.000 60 EVFGGGVGDI2.000 54 DPRETQEVFG 2.000 38 QGRAFRGSSV 2.000 25 NGECGQTFRL 1.200 2GKCQEYDKSL 0.400 42 FRGSSVHQKL 0.400 43 RGSSVHQKLV 0.200 57 ETQEVFGGGV0.200 10 SLSVQPEKRT 0.150 74 LSISFRNSET 0.100 69 IVGRDLSISF 0.100 76ISFRNSETSA 0.100 70 VGRDLSISFR 0.100 19 TGLRDENGEC 0.100 20 GLRDENGECG0.100 14 QPEKRTGLRD 0.060 52 VNDPRETQEV 0.060 4 CQEYDKSLSV 0.060 46SVHQKLVNDP 0.050 51 LVNDPRETQE 0.050 67 GDIVGRDLSI 0.040 41 AFRGSSVHQK0.030 37 EQGRAFRGSS 0.030 40 RAFRGSSVHQ 0.030 16 EKRTGLRDEN 0.030 50KLVNDPRETQ 0.023 33 RLKEEQGRAF 0.020 77 SFRNSETSAS 0.020 44 GSSVHQKLVN0.020 75 SISFRNSETS 0.020 68 DIVGRDLSIS 0.020 3 KCQEYDKSLS 0.020 82ETSASEEEKY 0.020 1 MGKCQEYDKS 0.020 61 VFGGGVGDIV 0.020 85 ASEEEKYDMS0.018 27 ECGQTFRLKE 0.015 73 DLSISFRNSE 0.015 28 CGQTFRLKEE 0.010 24ENGECGQTFR 0.010 9 KSLSVQPEKR 0.010 30 QTFRLKEEQG 0.010 31 TFRLKEEQGR0.010 13 VQPEKRTGLR 0.010 83 TSASEEEKYD 0.010 11 LSVQPEKRTG 0.010 62FGGGVGDIVG 0.010 64 GGVGDIVGRD 0.010 29 GQTFRLKEEQ 0.010 48 HQKLVNDPRE0.010 45 SSVHQKLVND 0.010 32 FRLKEEQGRA 0.010 63 GGGVGDIVGR 0.010 18RTGLRDENGE 0.010 79 RNSETSASEE 0.010 49 QKLVNDPRET 0.010 66 VGDIVGRDLS0.009 80 NSETSASEEE 0.003 58 TQEVFGGGVG 0.003 22 RDENGECGQT 0.003 23DENGECGQTF 0.002 53 NDPRETQEVF 0.002 72 RDLSISFRNS 0.002 36 EEQGRAFRGS0.002 81 SETSASEEEK 0.001 39 GRAFRGSSVH 0.001 7 YDKSLSVQPE 0.001 26GECGQTFRLK 0.001 5 QEYDKSLSVQ 0.001 47 VHQKLVNDPR 0.001 8 DKSLSVQPEK0.001 56 RETQEVFGGG 0.001 78 FRNSETSASE 0.001 17 KRTGLRDENG 0.001 59QEVFGGGVGD 0.001 71 GRDLSISFRN 0.001 34 LKEEQGRAFR 0.000 21 LRDENGECGQ0.000 35 KEEQGRAFRG 0.000 6 EYDKSLSVQP 0.000 86 SEEEKYDMSG 0.000 15PEKRTGLRDE 0.000 55 PRETQEVFGG 0.000 v.5-B7-10 mers: 213P1F11 2GARLALILRV 6.000 5 LALILRVTKA 0.300 8 ILRVTKAREG 0.100 10 RVTKAREGSE0.050 6 ALILRVTKAR 0.030 3 ARLALILRVT 0.030 4 RLALILRVTK 0.015 7LILRVTKARE 0.010 1 SGARLALILR 0.010 9 LRVTKAREGS 0.003 v.6-B7-10 mers:213P1F11 9 AMNNKNCQAL 12.000 8 EAMNNKNCQA 0.900 1 VKLENLFEAM 0.100 5NLFEAMNNKN 0.020 4 ENLFEAMNNK 0.010 10 MNNKNCQALR 0.010 2 KLENLFEAMN0.006 6 LFEAMNNKNC 0.003 3 LENLFEAMNN 0.002 7 FEAMNNKNCQ 0.001

[0767] TABLE XVII Pos 123456789 Score SeqID v.1-B35-9 mers: 213P1F11 123KPKVYIIQA 12.000 232 QSTLRKRLY 10.000 79 VSCAFVVLM 10.000 154 DSPQTIPTY10.000 94 FLKGEDGEM 9.000 121 RAKPKVYTT 7.200 223 KARKTNPEI 7.200 119ALRAKPKVY 6.000 73 DSREDPVSC 4.500 31 GSEEDLDAL 4.500 205 LLTEVTRRM4.000 77 DPVSCAFVV 4.000 170 STVEGYIAY 4.000 44 RQLRFESTM 4.000 195FTKRKGHIL 3.000 142 TVGGDEIVM 3.000 87 MAHGREGFL 3.000 151 VIKDSPQTI2.400 227 TNPEIQSTL 2.000 183 KGSCFTQTL 2.000 167 HVYSTVEGY 2.000 14MSGARLALI 2.000 155 SPQTIPTYT 2.000 6 SLEEEKYDM 1.800 135 EQRDPGETV1.200 231 IQSTLRKRL 1.000 233 STLRKRLYL 1.000 101 EMVKLENLF 1.000 158TIPTYTDAL 1.000 112 LNNKNCQAL 1.000 187 FIQTLVDVF 1.000 15 SGARLALIL1.000 184 GSCFIQTLV 1.000 86 LMAHGREGF 1.000 13 DMSGARLAL 1.000 16GARLALILC 0.900 57 TAEQFQEEL 0.900 169 YSTVEGYIA 0.750 118 QALRAKPKV0.600 3 NPRSLEEEK 0.600 104 KLENLFEAL 0.600 197 KRKGHILEL 0.600 164DALHVYSTV 0.600 143 VGGDEIVMV 0.600 49 ESTMKRDPT 0.500 161 TYTDALHVY0.400 138 DPGETVGGD 0.400 34 EDLDALEHM 0.400 201 HILELLTEV 0.400 27KAREGSEED 0.360 60 QFQEELEKF 0.300 35 DLDALEHMF 0.300 55 DPTAEQFQE 0.300210 TRRMAEAEL 0.300 5 RSLEEEKYD 0.300 226 KTNPEIQST 0.300 38 ALEHMFRQL0.300 30 EGSEEDLDA 0.300 144 GGDEIVMVI 0.240 141 ETVGGDEIV 0.200 199KGHILELLT 0.200 198 RKGHILELL 0.200 18 RLALILCVT 0.200 159 IPTYTDALH0.200 150 MVIKDSPQT 0.150 106 ENLFEALNN 0.150 64 ELEKFQQAIL 0.120 24CVTKAREGS 0.100 40 EHMFRQLRF 0.100 111 ALNNKNCQA 0.100 188 IQTLVDVFT0.100 147 EIVMVIKDS 0.100 78 PVSCAFVVL 0.100 208 EVTRRMAEA 0.100 100GEMVKLENL 0.100 20 ALILCVTKA 0.100 157 QTIPTYTDA 0.100 80 SCAFVVLMA0.100 50 STMKRDPTA 0.100 89 HGREGFLKG 0.060 228 NPEIQSTLR 0.060 70QAIDSREDP 0.060 95 LKGEDGEMV 0.060 211 RRMAEAELV 0.060 37 DALEHMFRQ0.060 11 KYDMSGARL 0.060 71 AIDSREDPV 0.060 53 KRDPTAEQF 0.060 179RHDQKGSCF 0.060 75 REDPVSCAF 0.060 1 MSNPRSLEE 0.050 9 EEKYDMSGA 0.045177 AYRHDQKGS 0.045 51 TMKRDPTAE 0.045 45 QLRFESTMK 0.045 102 MVKLENLFE0.045 131 ACRGEQRDP 0.045 97 GEDGEMVKL 0.045 180 HDQKGSCFI 0.040 168VYSTVEGYI 0.040 v.2-B35-9 mers: 213P1F11 10 TPFQDPLYL 30.000 8 GPTPFQDPL20.000 56 RGKDISWNF 12.000 44 HALSRPWWM 6.000 35 SPTDMIRKA 4.000 42KAHALSRPW 3.000 4 STVEGPTPF 2.000 22 APPNPPLWN 2.000 14 DPLYLPSEA 2.00046 LSRPWWMCS 1.500 53 CSRRGKDIS 1.500 21 EAPPNPPLW 1.500 38 DMIRKAHAL1.000 31 SQDTSPTDM 0.600 48 RPWWMCSRR 0.400 18 LPSEAPPNP 0.400 52MCSRRGKDI 0.400 39 MIRKAHALS 0.300 23 PPNPPLWNS 0.200 9 PTPFQDPLY 0.20026 PPLWNSQDT 0.200 25 NPPLWNSQD 0.200 54 SRRCKDTSW 0.150 17 YLPSEAPPN0.150 29 WNSQDTSPT 0.150 45 ALSRPWWMC 0.100 20 SEAPPNPPL 0.100 30NSQDTSPTD 0.100 34 TSPTDMIRK 0.075 3 YSTVEGPTP 0.075 43 AHALSRPWW 0.05032 QDTSPTDMI 0.040 55 RRGKDISWN 0.030 12 FQDPLYLPS 0.030 33 DTSPTDMIR0.010 27 PLWNSQDTS 0.010 37 TDMTRKAHA 0.010 2 VYSTVEGPT 0.010 51WMCSRRGKD 0.010 1 HVYSTVEGP 0.010 7 EGPTPFQDP 0.010 40 IRKALHALSR 0.0035 TVEGPTPFQ 0.003 41 RKAHALSRP 0.002 19 PSEAPPNPP 0.002 50 WWMCSRRGK0.001 24 PNPPLWNSQ 0.001 13 QDPLYLPSE 0.001 47 SRPWWMCSR 0.001 16LYLPSEAPP 0.001 6 VEGPTPFQD 0.001 15 PLYLPSEAP 0.001 28 LWNSQDTSP 0.00136 PTDMIRKAH 0.000 11 PFQDPLYLP 0.000 49 PWWMCSRRG 0.000 v.3-B35-9 mers11 LPSPFPYLS 2.000 9 ATLPSPFPY 2.000 7 RGATLPSPF 2.000 10 TLPSPFPYL1.000 3 IQACRGATL 1.000 12 PSPFPYLSL 0.500 5 ACRGATLPS 0.300 1 YIIQACRGA0.100 2 IIQACROAT 0.100 4 QACRGATLP 0.030 8 GATLPSPFP 0.030 6 CRGATLPSP0.001 v.4-B35-9 mers 54 DPRETQEVF 120.000 83 TSASEEEKY 15.000 85ASEEEKYDM 9.000 70 VGRDLSISF 6.000 3 KCQEYDKSL 4.000 13 VQPEKRTGL 2.00043 RGSSVHQKL 2.000 24 ENGECGQTF 2.000 33 RLKEEQGRA 1.800 44 GSSVHQKLV1.000 20 GLRDENGEC 0.900 76 ISFRNSETS 0.500 45 SSVHQKLVN 0.500 11LSVQPEKRT 0.500 68 DIVGRDLSI 0.400 38 QGRAFRGSS 0.300 66 VGDIVGRDL 0.30050 KLVNDPRET 0.300 62 FGGGVGDIV 0.200 69 ILVGRDLSIS 0.150 75 SISFRNSET0.100 37 EQGRAFRGS 0.100 73 DLSISFRNS 0.100 9 KSLSVQPEK 0.100 26GECGQTFRL 0.100 84 SASEEEKYD 0.090 40 RAFRGSSVH 0.060 14 QPEKRTGLR 0.06034 LKEEQGRAF 0.060 58 TQEVFGGGV 0.060 74 LSISFRNSE 0.050 4 CQEYDKSLS0.045 79 RNSETSASE 0.040 61 VFGGGVGDI 0.040 5 QEYDKSLSV 0.040 48HQKLVNDPR 0.030 77 SFRNSETSA 0.030 53 NDPRETQEV 0.030 1 MGKCQEYDK 0.03018 RTGLRDENG 0.020 51 LVNDPRETQ 0.020 39 GPAFRGSSV 0.020 72 RDLSISFRN0.020 57 ETQEVFGGG 0.020 17 KRTGLRDEN 0.020 65 GVGDIVGRD 0.020 23DENGECGQT 0.015 19 TGLRDENGE 0.015 12 SVQPEKRTG 0.015 80 NSETSASEE 0.01564 GGVGDIVGR 0.015 78 FRNSETSAS 0.015 2 GKCQEYDKS 0.015 46 SVHQKLVND0.010 28 CGQTFRLKE 0.010 29 GQTFRLKEE 0.010 30 QTFRLKEEQ 0.010 60EVFGGGVGD 0.010 82 ETSASEEEK 0.010 10 SLSVQPEKR 0.010 27 ECGQTFRLK 0.01063 GGGVGDIVG 0.010 67 GDIVGRDLS 0.010 86 SEEEKYDMS 0.006 16 EKRTGLRDE0.003 7 YDKSLSVQP 0.003 56 RETQEVFGG 0.003 41 AFRGSSVHQ 0.003 31TFRLKEEQG 0.003 52 VNDPRETQE 0.003 25 NGECGQTFR 0.003 32 FRLKEEQGR 0.00236 EEQGPAFRG 0.001 81 SETSASEEE 0.001 8 DKSLSVQPE 0.001 49 QKLVNDPRE0.001 47 VHQKLVNDP 0.001 42 FRGSSVHQK 0.001 59 QEVEGGGVG 0.001 22RDENGECGQ 0.001 21 LRDENGECG 0.001 35 KEEQGRAFR 0.001 15 PEKRTGLRD 0.00071 GRDLSISFR 0.000 6 EYDKSLSVQ 0.000 55 PRETQEVFG 0.000 v.5-B35-9 mers:213P1F11 9 RVTKAREGS 0.200 3 RLALILRVT 0.200 5 ALILRVTKA 0.100 1GARLALILR 0.090 7 ILRVTKARE 0.030 4 LALILRVTK 0.030 2 ARLALILRV 0.020 6LILRVTKAR 0.010 8 LRVTKAREG 0.001 v.6-B35-9 mers: 213P1F11 1 KLENLFEAM1.200 9 MNNKNCQAL 1.000 3 ENLFEAMNN 0.150 8 AMNNKNCQA 0.100 7 EAMNNKNCQ0.030 4 NLFEAMNNK 0.020 6 FEANNNKNC 0.010 2 LENLFEAMN 0.010 5 LFEAMNNKN0.003

[0768] TABLE XVIII Pos 1234567890 Score SeqID v.1-B35-10 mers: 213P1F113 NPRSLEEEKY 180.000 5 RSLEEEKYDM 60.000 27 KAREGSEEDL 36.000 77DPVSCAFVVL 20.000 123 KPKVYIIQAC 12.000 169 YSTVEGYIAY 10.000 37DALEHMFRQL 6.000 118 QALRAKPKVY 6.000 159 IPTYTDALHV 6.000 232QSTLRKRLYL 5.000 14 MSGARLALIL 5.000 30 EGSEEDLDAL 3.000 209 VTRRMAEAEL3.000 141 ETVGGDEIVM 3.000 73 DSREDPVSCA 3.000 204 ELLTEVTRRM 2.000 231IQSTLRKRLY 2.000 226 KTNPEIQSTL 2.000 96 KGEDGEMVKL 1.800 16 GARLALILCV1.800 59 EQFQEELEKF 1.500 119 ALRAKPKVYI 1.200 70 QAIDSREDPV 1.200 157QTIPTYTDAL 1.000 85 VLMAHGREGF 1.000 86 LMAHGREGFL 1.000 111 ALNNKNCQAL1.000 230 EIQSTLRKRL 1.000 94 FLKGEDGEMV 0.900 143 VGGDEIVMVI 0.800 197KRKGHILELL 0.600 52 MKRDPTAEQF 0.600 154 DSPQTIPTYT 0.500 79 VSCAFVVLMA0.500 49 ESTMKRDPTA 0.500 176 IAYRHDQKGS 0.450 193 DVFTKRKGHI 0.400 167HVYSTVEGYI 0.400 183 KGSCFIQTLV 0.400 13 DMSGARLALI 0.400 153 KDSPQTIPTY0.400 138 DPGETVGGDE 0.400 150 MVIKDSPQTI 0.400 142 TVGGDEIVMV 0.300 110EALNNKNCQA 0.300 196 TKRKGHILEL 0.300 113 NNKNCQALRA 0.300 19 LALILCVTKA0.300 102 MVKLENLFEA 0.300 99 DGEMVKLENL 0.300 181 DQKGSCFIQT 0.300 93GFLKGEDGEM 0.300 160 PTYTDALHVY 0.200 55 DPTAEQFQEE 0.200 10 EKYDMSGARL0.200 34 EDLDALEHMF 0.200 117 CQALRAKPKV 0.200 155 SPQTIPTYTD 0.200 56PTAEQFQEEL 0.200 205 LLTEVTRRMA 0.200 78 PVSCAFVVLM 0.200 218 LVQEGKARKT0.200 201 HILELLTEVT 0.200 107 NLFEALNNKN 0.200 185 SCFTQTLVDV 0.200 166LHVYSTVEGY 0.200 103 VKLENLFEAL 0.200 178 YRHDQKGSCF 0.200 43 FRQLRFESTM0.200 121 RAKPKVYIIQ 0.180 223 KARKTNPEIQ 0.180 149 VMVIKDSPQT 0.150 182QKGSCFIQTL 0.100 187 FIQTLVDVFT 0.100 186 CFIQTLVDVF 0.100 12 YDMSGARLAL0.100 194 VFTKRKGHIL 0.100 39 LEHMFRQLRF 0.100 100 GEMVKLENLF 0.100 41HMFRQLRFES 0.100 15 SGARLALILC 0.100 23 LCVTKAREGS 0.100 210 TRRMAEAELV0.090 215 EAELVQEGKA 0.090 133 RGEQRDPGET 0.090 63 EELEKFQQAIL 0.080 228NPEIQSTLRK 0.060 212 RMAEAELVQE 0.060 89 HGREGFLKGE 0.060 135 EQRDPGETVG0.060 151 VIKDSPQTIP 0.060 33 EEDLDALEHM 0.060 74 SREDPVSCAF 0.060 104KLENLFEALN 0.060 6 SLEEEKYDMS 0.060 1 MSNPRSLEEE 0.050 184 GSCFIQTLVD0.050 87 MAHGREGFLK 0.045 25 VTKAREGSEE 0.045 130 QACRGEQRDP 0.045v.2-B35-10 mers: 213P1F11 9 GPTPFQDPLY 40.000 31 NSQDTSPTDM 20.000 54CSRRGKDISW 7.500 4 YSTVEGPTPF 5.000 43 KAHALSRPWW 3.000 23 APPNPPLWNS2.000 26 NPPLWNSQDT 2.000 8 EGPTPFQDPL 1.000 35 TSPTDMIRKA 0.500 19LPSEAPPNPP 0.400 52 WMCSRRGKDI 0.400 36 SPTDMIRKAH 0.400 49 RPWWMCSRRG0.400 22 EAPPNPPLWN 0.300 45 HALSRPWWMC 0.300 15 DPLYLPSEAP 0.200 56RRGKDISWNF 0.200 11 TPFQDPLYLP 0.200 27 PPLWNSQDTS 0.200 44 AHALSRPWWM0.200 10 PTPFQDPLYL 0.150 20 PSEARPNPPL 0.150 47 LSRPWWMCSR 0.150 32SQDTSPTDMI 0.120 38 TDMIRKAHAL 0.100 2 HVYSTVEGPT 0.100 46 ALSRPWWMCS0.100 53 MCSRRGKDIS 0.100 39 DMIRKAHALS 0.100 42 RKAHALSRPW 0.100 21SEAPPNPPLW 0.050 55 SRRGKDISWN 0.045 40 MIRKAHALSR 0.030 5 STVEGPTPFQ0.020 24 PPNPPLWNSQ 0.020 17 LYLPSEAPPN 0.015 34 DTSPTDMIRK 0.015 29LWNSQDTSPT 0.015 30 WNSQDTSPTD 0.010 18 YLPSEAPPNP 0.010 14 QDPLYLPSEA0.010 41 TRKAHALSRP 0.003 13 FQDPLYLPSE 0.003 6 TVEGPTPFQD 0.003 37PTDMIRKAHA 0.003 12 PFQDPLYLPS 0.002 3 VYSTVEGPTP 0.002 25 PNPPLWNSQD0.001 7 VEGPTPFQDP 0.001 48 SRPWWMCSRR 0.001 51 WWMCSRRGKD 0.001 33QDTSPTDMIR 0.001 28 PLWNSQDTSP 0.001 16 PLYLPSEAPP 0.001 1 LHVYSTVEGP0.001 50 PWWMCSRRGK 0.000 v.3-B35-10 mers: 213P1F11 12 LPSPFPYLSL 20.0009 GATLPSPFPY 6.000 10 ATLPSPFPYL 1.000 3 IIQACRGATL 1.000 5 QACRGATLPS0.300 7 CRGATLPSPF 0.100 11 TLPSPFPYLS 0.100 2 YIIQACRGAT 0.100 6ACRGATLPSP 0.030 8 RGATLPSPFP 0.020 4 IQACRGATLP 0.010 1 VYIIQACRGA0.010 v.4-B35-10 mers: 213P1F11 84 SASEEEKYDM 18.000 33 RLKEEQGRAF12.000 82 ETSASEEEKY 3.000 65 GVGDIVGRDL 2.000 54 DPRETQEVFG 1.200 12SVQPEKRTGL 1.000 69 IVGRDLSISF 1.000 38 QGRAFRGSSV 0.600 3 KCQEYDKSLS0.600 74 LSISFRNSET 0.500 76 ISFRNSETSA 0.500 44 GSSVHQKLVN 0.500 1MGKCQEYDKS 0.450 57 ETQEVFGGGV 0.400 43 RGSSVHQKLV 0.400 60 EVFGGGVGDI0.400 85 ASEEEKYDMS 0.300 25 NGECGQTFRL 0.300 19 TGLRDENGEC 0.150 68DIVGRDLSIS 0.150 2 GKCQEYDKSL 0.100 37 EQGRAFRGSS 0.100 75 SISFRNSETS0.100 10 SLSVQPEKRT 0.100 53 NDPRETQEVF 0.100 9 KSLSVQPEKR 0.100 42FRGSSVHQKL 0.100 23 DENCECGQTF 0.100 52 VNDPRETQEV 0.090 83 TSASEEEKYD0.075 11 LSVQPEKRTG 0.075 20 GLRDENGECG 0.060 40 RAFRGSSVHQ 0.060 14QPEKRTGLRD 0.060 70 VGRDLSISFR 0.060 4 CQEYDKSLSV 0.060 45 SSVHQKLVND0.050 77 SFRNSETSAS 0.045 79 RNSETSASEE 0.040 67 GDIVGRDLSI 0.040 18RTCLRDENGE 0.030 16 EKRTGLRDEN 0.030 48 HQKLVNDPRE 0.030 66 VGDIVGRDLS0.030 24 ENGECGQTFR 0.020 61 VFGGGVGDIV 0.020 72 RDLSISFRNS 0.020 51LVNDPRETQE 0.020 50 KLVNDPRETQ 0.020 13 VQPEKRTGLR 0.020 80 NSETSASEEE0.015 49 QKLVNDPRET 0.015 32 FRLKEEQGRA 0.015 63 GGGVGDTVGR 0.015 64GGVGDTVGRD 0.010 30 QTFRLKEEQG 0.010 73 DLSISFRNSE 0.010 28 CGQTFRLKEE0.010 29 GQTFRLKEEQ 0.010 46 SVHQKLVNDP 0.010 62 FGGGVGDIVG 0.010 36EEQGRAFRGS 0.010 27 ECGQTFRLKE 0.010 22 RDENGECGQT 0.009 31 TFRLKEEQGR0.005 7 YDKSLSVQPE 0.003 41 AFRGSSVHQK 0.003 58 TQEVFGGGVG 0.003 71GRDLSISFRN 0.003 56 RETQEVFGGG 0.002 17 KRTGLRDENG 0.002 5 QEYDKSLSVQ0.002 47 VHQKLVNDPR 0.001 8 DKSLSVQPEK 0.001 26 GECGQTFRLK 0.001 81SETSASEEEK 0.001 78 FRNSETSASE 0.001 39 GRAFRGSSVH 0.001 59 QEVFGGGVGD0.001 21 LRDENGECGQ 0.001 34 LKEEQGRAFR 0.001 86 SEEEKYDMSG 0.001 35KEEQGRAFRG 0.001 15 PEKRTGLRDE 0.000 6 EYDKSLSVQP 0.000 55 PRETQEVFGG0.000 v.5-B35-10 mers: 213P1F11 2 GARLALILRV 1.800 5 LALILRVTKA 0.300 8TLRVTKAREG 0.030 4 RLALILRVTK 0.020 10 RVTKAREGSE 0.020 6 ALILRVTKAR0.010 7 LILRVTKARE 0.010 3 ARLALILRVT 0.010 9 LRVTKAREGS 0.010 1SGARLALILR 0.010 v.6-B35-10 mers: 213P1F11 9 AMNNKNCQAL 1.000 1VKLENLFEAM 0.400 8 EAMNNKNCQA 0.300 5 NLFEAMNNKN 0.200 2 KLENLFEAMN0.060 3 LENLFEAMNN 0.015 4 ENLFEAMNNK 0.010 10 MNNKNCQALR 0.010 6LFEAMNNKNC 0.003 7 FEAMNNKNCQ 0.001

[0769] TABLE XIXA MHC Class I Analysis of 213P1F11 (9-mers). Listed arescores which correlate with the ligation strength to a defined HLA typefor a sequence of amino acids. The algorithms used are based on the book“MHC Ligands and Peptide Motifs” by H. G. Rammensee, J. Bachmann and S.Stevanovic. The probability of being processed and presented is given inorder to predict T-cell epitopes. SEQ. Pos 1 2 3 4 5 6 7 8 9 score IDNO. TABLE XIXA, part 1: MHC Class 1 nonamer analysis of 213P1F11 v.1 (aa1-242). 213P1F11 v.1: HLA-A*0201 nonamers 201 H I L E L L T E V G 29 20A L I L C V G T K A 24 104 K L E N L F E A L 22 158 T I P T Y T D A L 2213 D M S G A R L A L 21 38 A L E H M F R Q L 21 17 A R L A L I L C V 2018 R L A L I L C V T 20 71 A I D S R E D P V 20 233 S T L R K R L Y L 20118 Q A L R A K P K V 19 121 R A K P K V Q T I 19 151 V I K D S P Q T I19 197 K R K G H I L E L 19 205 L L T E V T R R M 19 6 S L E E E K Y D M18 94 F L K G E D G E M 18 107 N L F E A L N N K 18 111 A L N N K N C QA 18 143 V G G G D E I V M V G 18 183 K G S C F I Q T L 18 186 C F I Q TL V D V G 18 202 I L E L L T E V T 18 226 K T N P E I Q S T 18 31 G S EE D L D A L 17 97 G E D G E M V K L 17 100 G E M V K L E N L 17 164 D AL H V Y S T V G 17 15 S G A R L A L I L 16 57 T A E Q F Q E E L 16 64 EL E K F Q Q A I 16 87 M A H G R E G F L 16 195 F T K R K G H I L 16 223K A R K T N P E I 16 86 L M A H G R E G F 15 103 V G K L E N L F E A 15120 L R A K P K V Y I 15 141 E T V G G D E I V G 15 144 G G D E I V M VI 15 234 T L R K R L Y L Q 15 14 M S G A R L A L I 14 21 L I L C V T K AR 14 22 I L C V T K A R E 14 50 S T M K R D P T A 14 85 V L M A H G R EG 14 95 L K G E D G E M V 14 112 L N N K N C Q A L 14 187 F I Q T L V GD V G F 14 198 R K G H I L E L L 14 21 T R R M A E A E L 14 227 T N P EI Q S T L 14 11 K Y D M S G A R L 13 19 L A L I L C V G T K 13 28 A R EG S E E D L 13 41 H H F R Q L R F E 13 78 P V S C A F V V L 13 227 Y I IQ A C R G E 13 160 P T Y T D A L H V 13 163 T D A L H V Y S T 13 165 A LH V Y S T V E 13 19 T L V D V G F T K R 13 204 E L L T E V T R R 13 212R M A E A E L V Q 13 214 A E A E L V Q E G 13 79 V S C A F V G V G L M12 80 S C A F V V L M A 12 119 A L R A K P K V Y 12 128 I I Q A C R G EQ 12 140 G E T V G G D E I 12 157 Q T I P T Y T D A 12 171 T V E G Y I AY R 12 189 Q T L V D V F T K 12 218 L V Q E G K A R K 12 231 I Q S T L RK R L 12 27 K A R E G S E E D 11 35 D L D A L E H M F 11 74 S R E D P VS C A 11 135 E Q R D P G E T V 11 150 M V I K D S P Q T 11 170 S T V E GY I A Y 11 175 Y I A Y R H D Q K 11 211 R R M A E A E L V 11 230 E I Q ST L R K R 11 81 C A F V V L M A H 10 142 T V G G D E I V M 10 149 V M VI K D S P Q 10 167 H V Y S T V E G Y 10 180 H D Q K G S C F I 10 184 G SC F I Q T L V 10 200 G H I L E L L T E 10 216 A E L V Q E G K A 10 12 YD M S G A R L A 9 16 G A R L A L I L C 9 44 R Q L R F E S T M 9 45 Q L RF E S T M K 9 46 L R F E S T M K R 9 76 E D P V S C A F V 9 77 D P V S CA F V V 9 123 K P K V Y I I Q A 9 148 I V M V I K D S P 9 153 K D S P QT I P T 9 162 Y T D A L H V Y S 9 168 V Y S T V E G Y I 9 176 I A Y R HD Q K G 9 206 L T E V T R R M A 9 213 M A E A E L V Q E 9 219 V Q E G KA R K T 9 2 S N P R S L E E E 8 34 E D L D A L E H M 8 51 T H K R D P TA E 8 52 M K R D P T A E Q 8 60 Q F Q E E L E K F 8 125 K V Y I I Q A CR 8 147 E I V M V I K D S 8 191 L V D V F T K R K 8 194 V F T K R K G HI 8 203 L E L L T E V T R 8 208 E V T R R M A E A 8 37 D A L E H M F R Q7 43 F R Q L R F E S T 7 56 P T A E Q F Q E E 7 67 K F Q Q A I D S R 770 Q A I D S R E D P 7 83 F V V L M A H G R 7 84 V V L M A H G R E 7 89H G R E G F L K G 7 90 G R E G F L K G E 7 101 E M V K L E N L F 7 134 GE Q R D P G E T 7 137 R D P G E T V G G 7 146 D E I V M V I K D 7 166 LH V Y S T V E G 7 188 I Q T L V D V F T 7 199 K G H I L E L L T 7 217 EL V Q E G K A R 7 222 G K A R K T N P E 7 1 M S N P R S L E E 6 25 V T KA R E G S E 6 63 E E L E K F Q Q A 6 93 G F L K G E D G E 6 105 L E N LF E A L N 6 114 N K N C Q A L R A 6 115 K N C Q A L R A K 6 134 Q A C RG E Q R D 6 138 D P G E T V G G D 6 154 D S P Q T I P T Y 6 155 S P Q TI P T Y T 6 169 Y S T V E G Y I A 6 185 S C F I Q T L V D 6 209 V T R RM A E A E 6 23 L C V T K A R E G 5 32 S E E D L D A L E 5 73 D S R E D PV S C 5 82 A F V V L M A H G 5 108 L F E A L N N K N 5 116 N C Q A L R AK P 5 161 T Y T D A L H V Y S 174 G Y I A Y R H D Q 5 178 Y R H D Q K GS C 5 193 D V F T K R K G H 5 7 L E E E K Y D M S 4 24 C V T K A R E G S4 26 T K A R E G S E E 4 30 E G S E E D L D A 4 36 L D A L E H M F R 469 Q Q A I D S R E D 4 102 M V K L E N L F E 4 110 E A L N N K N C Q 4129 I Q A C R G E Q R 4 131 A C R G E Q R D P 4 136 Q R D P G E T V G 4182 Q K G S C F I Q T 4 3 N P R S L E E E K 3 5 R S L E E E K Y D 3 39 LE H M F R Q L R 3 42 M F R Q L R F E S 3 53 K R D P T A E Q F 3 72 I D SR E D P V S 3 75 R E D P V S C A F 3 96 K G E D G E M V K 3 126 V Y I IQ A C R G 3 152 I K D S P Q T I P 3 61 F Q E E L E K F Q 2 65 L E K F QQ A I D 2 88 A H G R E G F L K 2 91 R E G F L K G E D 2 98 E D G E M V KL E 2 109 F E A L N N K N C 2 122 A K P K V Y I I Q 2 132 C R G E Q R DP G 2 145 G D E I V M V I K 2 156 P Q T I P T Y T D 2 159 I P T Y T D AL H 2 177 A Y R H D Q K G S 2 192 V D V F T K R K G 2 196 T K R K G H IL E 2 229 P E I Q S T L R K 2 48 F E S T M K R D P 1 49 E S T M K R D PT 1 58 A E Q F Q E E L E 1 68 F Q Q A I D S R E 1 99 D G E M V K L E N 1113 N N K N C Q A L R 1 117 C Q A L R A K P K 1 124 P K V Y I I Q A C 1133 R G E Q R D P G E 1 172 V E G Y T A Y R E 1 179 R H D Q K G S C F 1207 T E V T R R M A E 1 215 E A E L V Q E G K 1 220 Q E G K A R K T N 1224 A R K T N P E I Q 1 4 P R S L E E E K Y −1 8 E E E K Y D M S G −1 62Q E E L E K F Q Q −1 92 E G F L K G E D G −1 106 E N L F E A L N N −1228 N P E I Q S T L R −1 232 Q S T L R K R L Y −1 40 E H M F R Q L R F−2 47 R F E S T M K R D −2 55 D P T A E Q F Q E −2 66 E K F Q Q A I D S−2 173 E G Y I A Y R H D −2 139 P G E T V G G D E −4 221 E G K A R K T NP −4 213P1F11 v.1: HLA-A1 nonamers 170 S T V E G Y I A Y 29 232 Q S T LR K R L Y 21 154 D S P Q T I P T Y 19 99 D G E M V K L E N 18 119 A L RA K P K V Y 18 162 Y T D A L H V Y S 18 206 L T E V T R R M A 18 4 P R SL E E E K Y 17 136 Q R D P G E T V G 17 33 E E D L D A L E H 16 75 R E DP V S C A F 16 161 T Y T D A L H V Y 16 167 H V Y S T V E G Y 16 38 A LE H M F R Q L 15 233 S T L R K R L Y L 15 1 M S N P R S L E E 14 31 G SE E D L D A L 14 32 S E E D L D A L E 14 53 K R D P T A E Q F 14 74 S RE D P V S C A 14 104 K L E N L F E A L 14 219 V Q E G K A R K T 14 228 NP E I Q S T L R 14 6 S L E E E K Y D M 13 89 H G R E G F L K G 13 96 K GE D G E M V K 13 97 G E D G E M V K L 13 108 L F E A L N N K N 13 139 PG E T V G G D E 13 28 A R E G S E E D L 12 35 D L D A L E H M F 12 80 SC A F V V L M A 12 144 G G D E I V M V I 12 145 G D E I V M V I K 12 160P T Y T D A L H V 12 171 T V E G Y T A Y R 12 202 I L E L L T E V T 12215 E A E L V Q E G K 12 7 L E E E K Y D M S 11 8 E E E K Y D M S G 1111 K Y D M S G A R L 11 5 P T A E Q F Q E E 11 61 F Q E E L E K F Q 1164 E L E K F Q Q A I 11 71 A I D S R E D P V 11 90 G R E G F L K G E 11252 I K D S P Q T I P 11 179 R H D Q K G S C F 11 185 S C F I Q T L V D11 47 R F E S T M K R D 10 57 T A E Q F Q E E L 10 62 Q E E L E K F Q Q10 133 R G E Q R D P G E 10 153 K D S P Q T I P T 10 157 Q T I P T Y T DA 10 191 L V D V F T K R K 10 213 M A E A E L V Q E 10 226 K T N P E I QS T 10 141 E T V G G D E I V 9 13 D M S G A R L A L 8 15 S G A R L A L IL 8 50 S T M K R D P T A 8 79 V S C A F V V L M 8 114 N K N C Q A L R A8 190 T L V D V F T K R 8 195 F T K R K G H I L 8 196 T K R K G H I L E8 199 K G H I L E L L T 8 17 A R L A L I L C V 7 25 V T K A R E G S E 7102 M V K L E N L F E 7 122 A K P K V Y I I Q 7 146 D E I V M V I K D 7169 Y S T V E G Y I A 7 182 Q K G S C F I Q T 7 189 Q T L V D V F T K 7197 K R K G H I L E L 7 209 V T R R M A E A E 7 212 R M A E A E L V Q 712 Y D M S G A R L A 6 14 M S G A R L A L I 6 16 G A R L A L I L C 6 30E G S E E D L D A 6 40 E H M F R Q L R F 6 59 E Q F Q E E L E K 6 66 E KF Q Q A I D S 6 106 E N L F E A L N N 6 142 T V G G D E I V M 6 184 G SC F I Q T L V 6 200 G H I L E L L T E 6 229 P E I Q S T L R K 6 20 A L IL C V T K A 5 49 E S T M K R D P T 5 58 A E Q F Q E E L E 5 121 R A K PK V Y I I 5 123 K P K V Y I I Q A 5 216 A E L V Q E G K A 5 225 R K T NP E I Q S 5 5 R S L E E E K Y D 4 43 F R Q L R F E S T 4 73 D S R E D PV S C 4 78 P V S C A F V V L 4 88 A H G R E G F L K 4 165 A L H V Y S TV E 4 178 Y R I I D Q K G S C 4 39 L E H M F R Q L R 3 63 E E L E K F QQ A 3 85 V L M A H G R E G 3 8 L M A H G R E G F 3 94 F L K G E D G E M3 98 E D G E M V K L E 3 111 A L N N K N C Q A 3 116 N C Q A L R A K P 3126 V Y I I Q A C R G 3 132 C R G E Q R D P G 3 140 G E T V G G D E I 3168 V Y S T V E G Y I 3 187 F I Q T L V D V F 3 192 V D V F T K R K G 3205 L L T E V T R R M 3 234 T L R K R L Y L Q 3 2 S N P R S L E E E 2 18R L A L I L C V T 2 21 L I L C V T K A R 2 27 K A R E G S E E D 2 29 R EG S E E D L D 2 41 H M F R Q L R F E 2 45 Q L R F E S T M K 2 46 L R F ES T M K R 2 60 Q F Q E E L E K F 2 65 L E K F Q Q A I D 2 81 C A F V V LM A H 2 93 G F L K G E D G E 2 95 L K G E D G E M V 2 101 E M V K L E NL F 2 105 E N L F E A L N 2 109 F E A L N N K N C 2 113 N N K N C Q A LR 2 118 Q A L R A K P K V 2 127 Y I I Q A C R G E 2 130 Q A C R G E Q RD 2 131 A C R G E Q R D P 2 135 E Q R D P G E T V 2 143 V G G D E I V MV 2 147 E I V M V I K D S 2 155 S P Q T T P T Y T 2 159 I P T Y T D A LH 2 164 D A L H V Y S T V 2 174 G Y I A Y R H D Q 2 175 Y I A Y R H D QK 2 176 I A Y R H D Q K G 2 180 H D Q K G S C F I 2 188 I Q T L V D V FT 2 198 R K G H I L E L L 2 204 E L L T E V T R R 2 211 R R M A E A E LV 2 214 A E A E L V Q E G 2 217 E L V Q E G K A R 2 218 L V Q E G K A RK 2 230 E I Q S T L R K R 2 22 I L C V T K A R E 1 24 C V T K A R E G S1 26 T K A R E G S E E 1 42 M F R Q L R F E S 1 48 F E S T M K R D P 152 M K R D P T A E Q 1 68 F Q Q A I D S R E 1 70 Q A I D S R E D P 1 72I D S R E D P V S 1 77 D P V S C A F V V 1 82 A F V V L M A H G 1 83 F VV L M A H G R 1 84 V V L M A H G R E 1 87 M A H G R E G F L 1 92 E G F LK G E D G 1 103 V K L E N L F E A 1 107 N L F E A L N N K 1 120 L R A KP K V Y I 1 128 I I Q A C R G E Q 1 129 I Q A C R G E Q R 1 137 R D P GE T V G G 1 138 D P G E T V G G D 1 149 V M V I K D S P Q 1 151 V I K DS P Q T I 1 151 P Q T T P T Y T D 1 158 T I P T Y T D A L 1 163 T D A LH V Y S T 1 172 V E G Y I A Y R H 1 177 A Y R H D Q K G S 1 181 D Q K GS C F I Q 1 193 D V F T K R K G H 1 194 V F T K R K G H I 1 207 T E V TR R M A E 1 220 Q E G K A R K T N 1 223 K A R K T N P E I 1 224 A R K TN P E I Q 1 231 I Q S T L R K R L 1 213P1F11 v.1: HLA-A26 nonamers 35 DL D A L E H M F 27 170 S T V E G Y I A Y 27 167 H V Y S T V E G Y 26 187F I Q T L V D V F 25 60 Q F Q E E L E K F 23 78 P V S C A F V V L 23 154D S P Q T I P T Y 23 104 K L E N L F E A L 22 208 E V T R R M A E A 22230 E I Q S T L R K R 22 38 A L E H M F R Q L 21 34 E D L D A L E H M 2056 P T A E Q F Q E E 20 94 F L K G E D G E M 20 142 T V G G D E I V M 20147 E I V M V I K D S 20 158 T I P T Y T D A L 20 193 D V F T K R K G H20 195 F T K R K G H I L 20 119 A L R A K P K V Y 19 204 E L L T E V T RR 19 205 L L T E V T R R M 19 233 S T L R K R L Y L 19 6 S L E E E K Y DM 18 101 E M V K L E N L F 18 141 E T V G G D E I V 18 157 Q T I P T Y TD A 18 201 H I L E L L T E V 18 226 K T N P E I Q S T 18 13 D M S G A RL A L 17 40 E H M F R Q L R F 17 64 E L E K F Q Q A I 17 97 G E D G E MV K L 17 107 N L F E A L N N K 17 171 T V E G Y I A Y R 17 197 K R K G HI L E L 16 217 E L V Q E G K A R 16 20 A L I L C V T K A 15 31 G S E E DL D A L 15 63 E E L E K F Q Q A 15 150 M V I K D S P Q T 15 161 T Y T DA L H V Y 15 53 K R D P T A E Q F 14 75 R E D P V S C A F 14 100 G E M VK L E N L 14 127 Y I I Q A C R G E 14 151 V I K D S P Q T I 14 179 R H DQ K G S C F 14 186 C F I Q T L V D V 14 189 Q T L V D V F T K 14 190 T LV D V F T K R 14 218 L V Q E G K A R K 14 9 E E K Y D M S G A 13 18 R LA L I L C V T 13 37 D A L E H M F R Q 13 79 V S C A F V V L M 13 82 A FV V L M A H G 13 138 D P G E T V G G D 13 146 D E I V M V I K D 13 162 YT D A L H V Y S 13 283 K G S C F I Q T L 13 234 T L R K R L Y L Q 13 21K Y D M S G A R L 12 24 C V T K A R E G S 12 25 V T K A R E OS E 12 47 RF E S T M K R D 12 50 S T M K R D P T A 12 67 K F Q Q A I D S R 12 71 AI D S R E D P V 12 86 L M A H G R E G F 12 98 E D G E M V K L E 12 175 YI A Y R H D Q K 12 191 L V D V F T K R K 12 198 R K G H I L E L L 12 227T N P E I Q S T L 12 4 P R S L E E E K Y 11 21 L I L C V T K A R 11 28 AR E G S E E D L 11 83 F V V L M A H G R 11 84 V V L M A H G R E 11 102 MV K L E N L F E 11 112 L N N K N C Q A L 11 125 K V Y T I Q A C R 11 128I I Q A C R G E Q 11 148 I V M V I K D S P 11 160 P T Y T D A L H V 11164 D A L H V Y S T V 11 173 E G Y I A Y R H D 11 206 L T E V T R R M A11 209 V T R R M A E A E 11 15 S G A R L A L I L L 10 22 I L C V T K A RE 10 57 T A E Q F Q E E L 10 59 E Q F Q E E L E K 10 66 E K F Q Q A I DS 10 73 D S R E D P V S C 10 87 M A H G R E G F L 10 111 A L N N K N C QA 10 181 D Q K G S C F I Q 10 210 T R R M A E A E L 10 214 A E A E L V QE G 10 231 I Q S T L R K R L 10 232 Q S T L R K R L Y 10 8 E E E K Y D MS G 9 42 M F R Q L R F E S 9 44 R Q L R F E S T M 9 45 Q L R F E S T M K9 76 E D P V S C A F V 9 85 V L M A H G R E G 9 92 E G F L K G E D G 9202 T L E L L T E V T 9 7 L E E E K Y D M S 8 10 E K Y D M S G A R 8 30E G S E E D L D A 8 33 E E D L D A L E H 8 81 C A F V V L M A H 8 93 G FL K G E D G E 8 108 L F E A L N N K N 8 121 R A K P K V Y I I 8 144 G GD E I V M V I 8 165 A L H V Y S T V E 8 194 V F T K R K G H I 8 221 E GK A R K T N P 8 2 S H P R S L E E E 7 41 H M F R Q L R F E 7 46 L R F ES T M K R 7 49 E S T M K R D P T 7 55 D P T A E Q F Q E 7 77 D P V S C AF V V 7 89 H G R E G F L K G 7 90 G R E G F L K G E 7 99 D G E M V K L EN 7 103 V K L E N L F E A 7 106 E N L F E A L N N 7 135 E Q R D P G E TV 7 143 V G G D E I V M V 7 215 E A E L V Q E G K 7 74 S R E D P V S C A6 80 S C A F V V L M A 6 110 E A L N N K N C Q 6 115 K N C Q A L R A K 6122 A K P K V Y I I Q 6 123 K P K V Y I I Q A 6 124 P K V Y I I Q A C 6163 T D A L H V Y S T 6 182 Q K G S C F I Q T 6 200 G H I L E L L T E 6213 M A E A E L V Q E 6 14 M S G A R L A L I 5 17 A R L A L I L C V 5 43F R Q L R F E S T 5 137 R D P G E T V G G 5 145 G D E I V M V I K 5 229P E I Q S T L R K 5 16 G A R L A L I L C 4 70 Q A I D S R E D P 4 126 VY I T Q A C R G 4 219 V Q E G K A R K T 4 1 M S N P R S L E E 3 3 N P RS L E E E K 3 26 T K A R E G S E E 3 27 K A R E G S E E D 3 32 S E E D LD A L E 3 52 M K R D P T A E Q 3 61 F Q E E L E K F Q 3 65 L E K F Q Q AI D 3 95 L K G E D G E M V 3 116 N C Q A L R A K P 3 120 L R A K P K V YI 3 132 C R G E Q R D P G 3 133 R G E Q R D P G E 3 136 Q R D P G E T VG 3 153 K D S P Q T I P T 3 166 L H V Y S T V E G 3 178 Y R H D Q K G SC 3 185 S C F I Q T L V D 3 212 R M A E A E L V Q 3 223 K A R K T N P EI 3 5 R S L E E E K Y D 2 19 L A L I L C V T K 2 23 L C V T K A R E G 236 L D A L E H M F R 2 51 T M K R D P T A E 2 54 R D P T A E Q F Q 2 68F Q Q A I D S R E 2 69 Q Q A I D S R E D 2 91 R E G F L K G E D 2 96 K GE D G E M V K 2 109 F E A L N N K N C 2 113 N N K N C Q A L R 2 114 N KN C Q A L R A 2 118 Q A L R A K P K V 2 129 I Q A C R G E Q R 2 130 Q AC R G E Q R D 2 131 A C R G E Q R D P 2 149 V M V I K D S P Q 2 152 I KD S P Q T I P 2 174 G Y I A Y R H D Q 2 176 I A Y R H D Q K G 2 207 T EV T R R M A E 2 216 A E L V Q E G K A 2 222 G K A R K T N P E 2 12 Y D MS G A R L A 1 29 R E G S E E D L D 1 39 L E H M F R Q L R 1 58 A E Q F QE E L E 1 62 Q E E L E K F Q Q 1 72 I D S R E D P V S 1 105 L E N L F EA L N 1 117 C Q A L R A K P K 1 134 G E Q R D P G E T 1 140 G E T V G GD E I 1 159 I P T Y T D A L H 1 172 V E G Y I A Y R H 1 177 A Y R H D QK G S 1 180 H D Q K G S C F I 1 188 T Q T L V D V F T 1 192 V D V F T KR K G 1 196 T K R K G H I L E 1 199 K G H I D E L L T 1 203 L E L L T EV T R 1 220 Q E G K A R K T N 1 224 A R K T N P E I Q 1 225 R K T N P EI Q S 1 228 N P E I Q S T L R 1 213P1F11 v.1: HLA-A3 nonamers 119 A L RA K P K V Y 30 45 Q L R F E S TM K 27 218 L V QE G K AR K 26 125 K V YII Q AC R 25 175 Y I AY R H DQ K 24 19 L A LI L C VT K 21 96 K G ED G EMV K 21 107 N L FE A L NN K 21 18 R L AL I L CV T 20 167 H V YS T V EG Y20 191 L V DV F T KR K 20 88 A H GR E G FL K 19 171 T V EG Y I AY R 1920 A L IL C V TK A 18 78 P V SC A F VV L 18 83 F V VL M A HG R 18 111 AL NN K N CQ A 18 165 A L HV Y S TV E 18 189 Q T LV D V FT K 18 208 E VTR R M AE A 18 217 E L VQ E G KA R 18 35 D L DA L E HM F 17 217 C Q AL RA KP K 17 290 T L VD V F TK R 17 202 I L EL L T EV T 17 204 E L LT E VTR R 17 21 L I LC V T KA R 16 38 A L EH M F RQ L 16 44 R Q LR F E ST M16 53 K R DP T A EQ F 16 142 T V GG D E IV M 16 145 G D EI V M VI K 16150 M V IK D S PQ T 16 187 F I QT L V DV F 16 193 D V FT K R KG H 16 229P E IQ S T LR K 16 22 I L CV T K AR E 15 85 V L MA H G RE G 15 102 M VKL E N LF E 15 104 K L EN L F EA L 15 129 I Q AC R G EQ R 15 151 V I KDS P QT I 15 179 R H DQ K G SC F 15 203 L E LL T E VT R 15 234 T L RK R LYL Q 15 94 F L KG E D GE M 14 115 K N CQ A L RA K 14 128 I I QA C R GE Q14 148 I V MV I K DS P 14 3 N P RS L E EE K 13 59 E Q FQ E E LE K 13 71A I DS R E DP V 13 75 R E DP V S CA F 13 84 V V LM A H GR E 13 212 R MAE A E LV Q 13 6 S L EE E K YD H 12 136 Q R DP G E TV G 12 201 H I LE LL TE V 12 205 L L TE V T RR M 12 215 E A EL V Q EG K 12 230 E I QS T LRK R 12 10 E K YD M S GA R 11 15 S G AR L A LI L 11 24 C V TK A R EG S11 33 E E DL D A LE H 11 64 E L EK F Q QA I 11 73 D S RE D P VS C 11 127Y I IQ A C RG E 11 135 E Q RD P G ET V 11 161 T Y TD A L HV Y 11 170 S TVE G Y IA Y 11 200 G H IL E L LT E 11 232 Q S TL R K RL Y 11 233 S T LRK R LY L 11 17 A R LA L I LC V 10 26 T K AR E G SE E 10 137 R D PG E TVG G 10 154 D S PQ T I PT Y 10 160 P T YT D A LH V 10 164 D A LH V Y STV 10 209 V T RR M A EA E 10 11 K Y DM S G AR L 9 27 K A RE G S EE D 9 40E H MF R Q LR F 9 67 K F QQ A I DS R 9 72 I D SR E D PV S 9 89 H G RE GF LK G 9 113 N N KN C Q AL R 9 121 R A KP K V YI I 9 147 E I VM V T KD S9 157 Q T IP T Y TD A 9 158 T I PT Y T DA L 9 159 I P TY T D AL H 9 176I A YR H D QK G 9 185 S C FI Q T LV D 9 197 K R KG H I LE L 9 211 R R MAE A EL V 9 213 M A EA E L VQ E 9 1 M S NP R S LE E 8 25 V T KA R E GS E8 86 L M AH G R EG F 8 106 E N LF E A LN N 8 131 A C RG E Q RD P 8 188 IQ TL V D VF T 8 195 F T KR K G HI L 8 225 R K TN P E IQ S 8 226 K T NP EI QS T 8 227 T N PE I Q ST L 8 4 P R SL E E EK Y 7 5 R S LE E E KY D 713 D M SG A R LA L 7 14 M S GA R L AL I 7 36 L D AL E H MF R 7 50 S T MKR D PT A 7 51 T M KR D P TA E 7 52 M K RD P T AE Q 7 60 Q F QE E L EK F7 63 E E LE K F QQ A 7 70 Q A ID S R ED P 7 77 D P VS C A FV V 7 80 S CAF V V LM A 7 81 C A FV V L MA H 7 118 Q A LR A K PK V 7 123 K P KV Y IIQ A 7 126 V Y II Q A CR G 7 130 Q A CR G E QR D 7 172 V E GY I A YR H 7183 K G SC F I QT L 7 186 C F IQ T L VD V 7 199 K G HI L ELL T 7 220 Q EGK A RKT N 7 46 L R FE S TMK R 6 62 Q E EL E KFQ Q 6 79 V S CA F VVL M 682 A F VV L M AH G 6 97 G E DG E M VK L 6 114 N K NC Q A LR A 6 116 N CQA L R AK P 6 133 R G EQ R D PG E 6 143 V G GD E I VM V 6 144 G G DE I VMV I 6 153 K D SP Q T TP T 6 162 Y T DA L H VY S 6 174 G Y IA Y R HD Q 6177 A Y RH D Q KG S 6 210 T R RM A E AE L 6 216 A E LV Q E GK A 6 219 VQ EG K A RK T 6 221 E G KA R K TN P 6 223 K A RK T N PE I 6 228 N P EI QS TL R 6 12 Y D MS G A RL A 5 28 A R EG S E ED L 5 32 S E ED L D AL E 539 L E HM F R QL R 5 43 F R QL R F ES T 5 55 D P TA E Q FQ E 5 68 F Q QAI D SR E 5 74 S R ED P V SC A 5 87 M A HG R E GF L 5 91 R E GF L K GE D5 92 E G FL K G ED G 5 95 L K GE D G EM V 5 120 L R AK P K VY I 5 134 GE QR D P GE T 5 139 P G ET V G GD E 5 140 G E TV G G DE I 5 149 V M VI KD SP Q 5 156 P Q TI P T YT D 5 173 E G YI A Y RH D 5 182 Q K GS C F IQ T5 196 T K RK G H IL E 5 207 T E VT R R MA E 5 214 A E AE L V QE G 5 222G K AR K T NP E 5 224 A R KT N P EI Q 5 2 S N PR S L EE E 4 9 E E KY D MSG A 4 16 G A RL A L IL C 4 23 L C VT K A RE G 4 29 R E GS E E DL D 4 30E G SE E D LD A 4 42 M F RQ L R FE S 4 47 R F ES T M KR D 4 54 R D PT AE QF Q 4 65 L E KF Q Q AT D 4 69 Q Q AI D S RE D 4 93 G F LK G E DG E 499 D G EM V K LE N 4 101 E M VK L E NL F 4 105 L E NL F E AL N 4 122 A KPK V Y II Q 4 141 E T VG G D EI V 4 163 T D AL H V YS T 4 166 L H VY S TVE G 4 178 Y R HD Q K GS C 4 198 R K GH I L EL L 4 7 L E EE K Y DM S 3 8E E EK Y D MS G 3 34 E D LD A L EH H 3 37 D A LE H MF R Q 3 41 H M FR QLR F E 3 58 A E QF Q EE L E 3 66 E K FQ Q A ID S 3 76 E D PV S C AF V 3103 V K LE N L FE A 3 110 E A LN N K NC Q 3 146 D E IV M V IK D 3 152 IK DS P Q TI P 3 155 S P QT I P TY T 3 169 Y S TV E G YI A 3 181 D Q KG SC FI Q 3 194 V F TK R K GH I 3 231 I Q ST L R KR L 3 31 G S EE D L DA L2 49 E S TM K R DP T 2 56 P T AE Q F QE E 2 90 G R EG F L KG E 2 108 L FEA L N NK N 2 109 F E AL N N KN C 2 132 C R GE Q R DP G 2 138 D P GE T VGG D 2 168 V Y ST V E GY I 2 180 H D QK G S CF I 2 206 L T EV T R RM A 261 F Q EE L E KF Q 1 98 E D GE M V KL E 1 100 G E MV K L EN L 1 112 L NNK N C QA L 1 124 P K VY I I QA C 1 184 G S CF I Q TL V 1 213P1F11 v.1:HLA-B*0702 nonamers 13 D H S G A R L A L 18 77 D P V S C A F V V 17 123K P K V Y I T Q A 17 155 S P Q T I P T Y T 17 78 P V S C A F V V L 16 97G E D G E M V K L 15 197 K R K G H I L E L 15 11 K Y D M S G A R L 14 28A R E G S E E D L 14 231 I Q S T L R K R L 14 15 S G A R L A L I L 13 38A L E H M F R Q L 13 87 M A H G R E G F L 13 104 K L E N L F E A L 13120 L R A K P K V Y I 13 135 E Q R D P G E T V 13 183 K G S C F I Q T L13 210 T R R M A E A E L 13 233 S T L R K R L Y L 13 3 N P R S L E E E K12 112 L N N K N C Q A L 12 138 D P G E T V G G D 12 153 K D S P Q T I PT 12 158 T I P T Y T D A L 12 159 I P T Y T D A L H 12 198 R K G H I L EL L 12 17 A R L A L I L C V 11 30 E G S E E D L D A 11 31 G S E E D L DA L 11 55 D P T A E Q F Q E 11 100 G E M V K L E N L 11 195 F T K R K GH I L 11 223 K A R K T N P E I 11 228 N P E I Q S T L R 11 20 A L I L CV T K A 10 40 E H M F R Q L R F 10 57 T A E Q F Q E E L 10 71 A I D S RE D P V 10 74 S R E D P V S C A 10 75 R E D P V S C A F 10 79 V S C A FV V L M 10 80 S C A F V V L M A 10 242 T V G G D E I V M 10 188 I Q T LV D V F T 10 227 T N P E I Q S T L 10 14 M S G A R L A L I 9 18 R L A LI L C V T 9 49 E S T M K R D P T 9 50 S T M K R D P T A 9 53 K R D P T AE Q F 9 64 E L E K F Q Q A I 9 76 E D P V S C A F V 9 121 R A K P K V YI I 9 141 E T V G G D E I V 9 143 V G G D E I V M V 9 144 G G D E I V MV I 9 179 R H D Q K G S C F 9 199 K G H I L E L L T 9 202 I L E L L T EV T 9 211 R R M A E A E L V 9 35 D L D A L E H M F 8 63 E E L E K F Q QA 8 86 L M A H G R E G F 8 94 F L K G E D G E M 8 95 L K G E D G E M V 8101 E M V K L E N L F 8 111 A L N N K N C Q A 8 114 N I C N C Q A L R A8 150 M V I K D S P Q T 8 157 Q T I P T Y T D A 8 160 P T Y T D A L H V8 163 T D A L H V Y S T 8 168 V Y S T V E G Y I 8 180 H D Q K G S C F I8 182 Q K G S C F T Q T 8 186 C F I Q T L V D V 8 187 F I Q T L V D V F8 208 E V T R R M A E A 8 216 A E L V Q E G K A 8 219 V Q E G K A R K T8 226 K T N P E I Q S T 8 9 E E K Y D M S G A 7 12 Y D M S G A R L A 734 E D L D A L E H M 7 43 F R Q L R F E S T 7 44 R Q L R F E S T M 7 52M K R D P T A E Q 7 118 Q A L R A K P K V 7 140 G E T V G G D E I 7 169Y S T V E G Y I A 7 184 G S C F I Q T L V 7 194 V F T K R K G H I 7 201H I L E L L T E V 7 205 L L T E V T R R M 7 206 L T E V T R R M A 7 6 SL E E E K Y D M 6 60 Q F Q E E l E K F 6 103 V K L E N L F E A 6 119 A LR A K P K V Y 6 131 A C R G E Q R D P 6 134 G E Q R D P G E T 6 137 R DP G E T V G G 6 151 V I K D S P Q T I 6 152 I L K D S P Q T I P 6 164 DA L H V Y S T V 6 72 I D S R E D P V S 5 89 H G R E G F L K G 5 212 R MA E A E L V Q 5 33 E E D L D A L E H 4 73 D S R E D P V S C 4 88 A H G RE G F L K 4 136 Q R D P G E T V G 4 156 P Q T I P T Y T D 4 162 Y T D AL H V Y S 4 165 A L H V Y S T V E 4 177 A Y R H D Q K G S 4 185 S C F IQ T L V D 4 214 A E A E L V Q E G 4 225 R K T N P E I Q S 4 1 M S N P RS L E E 3 27 K A R E G S E E D 3 42 M F R Q L R F E S 3 45 Q L R F E S TM K 3 59 E Q F Q E E L E K 3 82 A F V V L M A H G 3 85 V L M A H G R E G3 98 E D G E M V K L E 3 102 M V K L E N L F E 3 106 E N L F E A L N N 3116 N C Q A L R A K P 3 122 A K P K V Y I I Q 3 128 I I Q A C R G E Q 3129 I Q A C R G E Q R 3 132 C R G E Q R D P G 3 166 L H V Y S T V E G 3171 T V E G Y I A Y R 3 196 T K R K G H I L E 3 204 E L L T E V T R R 3209 V T R R M A E A E 3 213 M A E A E L V Q E 3 217 E L V Q E G K A R 3220 Q E G K A R K T N 3 221 E G K A R K T N P 3 222 G K A R K T N P E 3229 P E I Q S T L R K 3 234 T L R K R L Y L Q 3 4 P R S L E E E K Y 2 8E E E K Y D M S G 2 10 E K Y D M S G A R 2 16 G A R L A L I L C 2 19 L AL I L C V T K 2 21 L I L C V T K A R 2 22 I L C V T K A R E 2 24 C V T KA R E G S 2 26 T K A R E G S E E 2 29 R E G S E E D L D 2 36 L D A L E HM F R 2 48 F E S T M K R D P 2 51 T M K R D P T A E 2 54 R D P T A E Q FQ 2 56 P T A E Q F Q E E 2 58 A E Q F Q E E L E 2 90 G R E G F L K G E 291 R E G F L K G E D 2 92 E G F L K G E D G 2 96 K G E D G E M V K 2 99D G E M V K L E N 2 115 K N C Q A L R A K 2 117 C Q A L R A K P K 2 125K V Y I I Q A C R 2 133 R G E Q R D P G E 2 145 G D E I V M V I K 2 148T V M V I K D S P 2 174 G Y I A Y R H D Q 2 181 D Q K G S C F I Q 2 190T L V D V F T K R 2 191 L V D V F T K R K 2 200 G H I L E L L T E 2 203L E L L T E V T R 2 207 T E V T R R M A E 2 224 A R K T N P E I Q 2 5 RS L E E E K Y D 1 25 V T K A R E G S E 1 32 S E E D L D A L E 1 39 L E HM F R Q L R 1 41 H M F R Q L R F E 1 46 L R F E S T M K R 1 47 R F E S TM K R D 1 61 F Q E E L E K F Q 1 65 L E K F Q Q A I D 1 66 E K F Q Q A ID S 1 67 K F Q Q A T D S R 1 68 F Q Q A I D S R E 1 69 Q Q A I D S R E D1 70 Q A I D S R E D P 1 81 C A F V V L M A H 1 93 G F L K G E D G E 1105 L E N L F E A L N 1 108 L F E A L N N K N 1 109 F E A L N N K N C 1110 E A L N N K N C Q 1 113 N N K N C Q A L R 1 124 P K V Y I I Q A C 1139 P G E T V G G D E 1 146 D E I V M V I K D 1 247 E I V M V I K D S 1249 V M V I K D S P Q 1 254 D S P Q T I P T Y 1 261 T Y T D A L H V Y 1267 H V Y S T V E G Y 1 270 S T V E G Y I A Y 1 272 V E C Y I A Y R H 1273 E G Y I A Y R H D 1 275 Y I A Y R H D Q K 1 276 I A Y R H D Q K G 1289 Q T L V D V F T K 1 293 D V F T K R K G H 1 215 E A E L V Q E G K 1218 L V Q E G K A R K 1 230 E I Q S T L R K R 1 213P1F11 v.1: HLA-B*08nonamers 121 R A K P K V Y I I 31 195 F T K R K G H I L 31 119 A L R A KP K V Y 23 87 M A H G R E G F L 22 100 G E M V K L E N L 22 197 K R K GH I L E L 22 233 S T L R K R L Y L 22 151 V I K D S P Q T I 21 221 E G KA R K T N P 20 234 T L R K R L Y L Q 20 25 V T K A R E G S E 19 94 F L KG E D C E M 18 123 K P K V Y I I Q A 18 223 K A R K T N P E I 18 104 K LE N L F E A L 17 111 A L N N K N C Q A 17 210 T R R M A E A E L 17 38 AL E H M F R Q L 16 40 E H M F R Q L R F 16 179 R H D Q K G S C F 16 57 TA E Q F Q E E L 15 64 E L E K F Q Q A I 15 158 T I P T Y T D A L 15 194V F T K R K G H I 15 14 M S G A R L A L I 14 31 G S E E D L D A L 14 63E E L E K F Q Q A 14 3 N P R S L E E E K 13 9 E E K Y D M S G A 13 27 KA R E G S E E D 13 92 E G F L K G E D G 13 175 Y I A Y R H D Q K 13 7 LE E E K Y D M S 12 15 S G A R L A L I L 12 16 G A R L A L I L C 12 35 DL D A L E H M F 12 45 Q L R F E S T M K 12 49 E S T M K R D P T 12 71 AI D S R E D P V 12 97 G E D G E M V K L 12 102 M V K L E N L F E 12 187F I Q T L V D V F 12 227 T N P E I Q S T L 12 231 T Q S T L R K R L 1213 D M S G A R L A L 11 23 L C V T K A R E G 11 51 T M K R D P T A E 1178 P V S C A F V V L 11 112 L N N K N C Q A L 11 149 V M V I K D S P Q11 183 K G S C F I Q T L 11 193 D V F T K R K G H 11 208 E V T R R M A EA 11 219 V Q E G K A R K T 11 222 G K A R K T N P E 11 6 S L E E E K Y DM 10 11 K Y D M S G A R L 10 28 A R E G S E E D L 10 43 F R Q L R F E ST 10 50 S T M K R D P T A 10 65 L E K F Q Q A I D 10 113 N N K N C Q A LR 10 117 C Q A L R A K P K 10 144 G C D E I V M V I 10 181 D Q K G S C FI Q 10 198 R K G H I L E L L 10 217 E L V Q E G K A R 10 224 A R K T N PE I Q 10 1 M S N P R S L E E 9 73 D S R E D P V S C 9 89 H G R E G F L KG 9 129 I Q A C R G E Q R 9 138 D P G E T V G G D 9 140 G E T V G G D EI 9 204 E L L T E V T R R 9 207 T E V T R R M A E 9 232 Q S T L R K R LY 9 20 A L I L C V T K A 8 22 I L C V T K A R E 8 60 Q F Q E E L E K F 885 V L M A H G R E Q 8 101 E M V K L E N L F 8 107 N L F E A L N N K 8133 R G E Q R D P G E 8 135 E Q R D P G E T V 8 147 E I V M V I K D S 8155 S P Q T I P T Y T 8 159 I P T Y T D A L H 8 201 H I L E L L T E V 8202 I L E L L T E V T 8 205 L L T E V T R R M 8 209 V T R R M A E A E 818 R L A L I L C V T 7 42 M F R Q L R F E S 7 52 M K R D P T A E Q 7 75R E D P V S C A P 7 120 L R A K P K V Y I 7 165 A L H V Y S T V E 7 168V Y S T V E G Y I 7 177 A Y R H D Q K G S 7 180 H D Q K G S C F I 7 215E A E L V Q E G K 7 21 L I L C V T K A R 6 37 D A L E H M F R Q 6 53 K RD P T A E Q F 6 55 D P T A E Q F Q E 6 77 D P V S C A F V V 6 81 C A F VV L M A H 6 86 L M A H G R E G F 6 98 E D G E M V K L E 6 110 E A L N NK N C Q 6 128 I I Q A C R G E Q 6 131 A C R G E Q R D P 6 190 T L V D VF T K R 6 196 T K R K G H I L E 6 228 N P E I Q S T L R 6 230 E I Q S TL R K R 6 19 L A L I L C V T K 5 170 S T V E G Y I A Y 5 176 I A Y R H DQ K G S 213 M A E A E L V Q E 5 30 E G S E E D L D A 4 33 E E D L D A LE H 4 61 F Q E E L E K F Q 4 70 Q A I D S R E D P 4 103 V K L E N L F EA 4 109 F E A L N N K N C 4 118 Q A L R A K P K V 4 127 Y I I Q A C R GE 4 130 Q A C R G E Q R D 4 164 D A L H V Y S T V 4 214 A E A E L V Q EG 4 2 S N P R S L E E E 3 5 R S L E E E K Y D 3 10 E K Y D M S G A R 356 P T A E Q F Q E E 3 59 E Q F Q E E L E K 3 74 S R E D P V S C A 3 76E D P V S C A F V 3 79 V S C A F V V L M 3 80 S C A F V V L M A 3 124 PK V Y I I Q A C 3 143 V G G D E I V M V 3 166 L H V Y S T V E G 3 188 IQ T L V D V F T 3 8 E E E K Y D M S G 2 32 S E E D L D A L E 2 34 E D LD A L E H H 2 46 L R F E S T M K R 2 66 E K F Q Q A I D S 2 83 F V V L MA H G R 2 90 G R E G F L K G E 2 95 L K G E D G E M V 2 106 E N L F E AL N N 2 132 C R G E Q R D P G 2 134 G E Q R D P G E T 2 141 E T V G G DE I V 2 145 G D E I V M V I K 2 146 D E I V M V I K D 2 148 I V M V I KD S P 2 163 T D A L H V Y S T 2 167 H V Y S T V E G Y 2 172 V E G Y I AY R H 2 173 E G Y T A Y R H D 2 185 S C F I Q T L V D 2 189 Q T L V D VF T K 2 191 L V D V F T K R K 2 200 G H I L E L L T E 2 203 L E L L T EV T R 2 212 R M A E A E L V Q 2 218 L V Q E G K A R K 2 4 P R S L E E EK Y 1 17 A R L A L I L C V 1 26 T K A R E G S E E 1 36 L D A L E H M F R1 41 H M F R Q L R F E 1 47 R F E S T M K R D 1 48 F E S T H K R D P 162 Q E E L E K F Q Q 1 67 K F Q Q A I D S R 1 68 F Q Q A I D S R E 1 69Q Q A I D S R E D 1 72 I D S R E D P V S 1 82 A F V V L M A H G 1 84 V VL M A H G R E 1 91 R E G F L K G E D 1 93 G F L K G E D G E 1 99 D G E MV K L E N 1 105 L E N L F E A L N 1 108 L F E A L N N K N 1 115 K N C QA L R A K 1 126 V Y I I Q A C R G 1 137 R D P G E T V G G 1 152 I K D SP Q T I P 1 154 D S P Q T I P T Y 1 162 Y T D A L H V Y S I 169 Y S T VE G Y I A 1 171 T V E G Y I A Y R 1 174 G Y I A Y R H D Q 1 184 G S C FI Q T L V 1 186 C F I Q T L V D V 1 192 V D V F T K R K G 1 206 T V E VT R R M A 1 216 A E L V Q E G K A 1 220 Q E G K A R K T N I 226 K T N PE I Q S T 1 213P1F11 v.1: HLA-B*1510 nonamers 40 E H M F R Q L R F 19179 R H D Q K G S C F 17 231 I Q S T L R K R L 16 78 P V S C A F V V L15 97 G E D G E M V K L 15 13 D H S G A R L A L 14 31 G S E E D L D A L14 57 T A E Q F Q E E L 14 38 A L E H M F R Q L 13 112 L N N K N C Q A L13 166 L H V Y S T V E G 13 183 K G S C F I Q T L 13 197 K R K G H I L EL 13 227 T N P E I Q S T L 13 11 K Y D M S G A R L 12 28 A R E G S E E DL 12 100 G E M V K L E N L 12 104 K L E N L F E A L 12 158 T I P T Y T DA L 12 200 G H I L L E L L T E 12 210 T R R M A E A E L 12 15 S G A R LA L I L 11 87 M A H G R E G F L 11 205 L L T E V T R R M 11 233 S T L RK R L Y L 11 88 A H G R E G F L K 10 142 T V G G D E I V M 10 195 F T KR K G H I L 10 198 R K G H I L E L L 10 6 S L E E E K Y D M 9 75 R E D PV S C A F 9 79 V S C A F V V L M 9 86 L M A H G R E G F 9 187 F I Q T LV D V F 9 34 E D L D A L E H M 8 53 K R D P T A E Q F 8 94 F L K G E D GE H 8 101 E H V K L E N L F 8 44 R Q L R F E S T M 7 60 Q F Q E E L E KF 7 22 I L C V T K A R E 6 35 D L D A L E H M F 6 72 I D S R E D P V S 6120 L R A K P K V Y I 6 96 K G E D G E M V K 5 136 Q R D P G E T V G 5144 G G D E I V M V I 5 145 G D E I V M V I K 5 202 I L E L L T E V T 5206 L T E V T R R M A 5 218 L V Q E G K A R K 5 12 Y D M S G A R L A 437 D A L E H M F R Q 4 47 R F E S T M K R D 4 48 F E S T M K R D P 4 64E L E K F Q Q A I 4 69 Q Q A I D S R E D 4 73 D S R E D P V S C 4 74 S RE D P V S C A 4 115 K N C Q A L R A K 4 127 Y I I Q A C R G E 4 128 I IQ A C R G E Q 4 135 E Q R D P G E T V 4 140 G E T V G G D E I 4 143 V GG D E I V M V 4 148 I V M V I K D S P 4 154 D S P Q T I P T Y 4 161 T YT D A L H V Y 4 171 T V E G Y I A Y R 4 188 I Q T L V D V F T 4 204 E LL T E V T R R 4 212 R M A E A E L V Q 4 214 A E A E L V Q E G 4 219 V QE G K A R K T 4 1 M S N P R S L E E 3 8 E E E K Y D M S G 3 10 E K Y D MS G A R 3 18 R L A L I L C V T 3 19 L A L I L C V T K 3 23 L C V T K A RE G 3 26 T K A R E G S E E 3 27 K A R E G S E E D 3 30 E G S E E D L D A3 42 M F R Q L R F E S 3 50 S T M K R D P T A 3 51 T M K R D P T A E 352 M K R D P T A E Q 3 56 P T A E Q F Q E E 3 59 E Q F Q E E L E K 3 85V L M A H G R E G 3 90 G R E G F L K G E 3 93 G F L K G E D G E 3 98 E DG E M V K L E 3 99 D G E M V K L E N 3 103 V K L E N L F E A 3 110 E A LN N K N C Q 3 119 A L R A K P K V Y 3 121 R A K P K V Y I I 3 129 I Q AC R G E Q R 3 130 Q A C R G E Q R D 3 131 A C R G E Q R D P 3 133 R G EQ R D P G E 3 134 G E Q R D P G E T 3 137 R D P G E T V G G 3 141 E T VG G D E I V 3 151 V I K D S P Q T I 3 152 I K D S P Q T I P 3 153 K D SP Q T I P T 3 162 Y T D A L H V Y S 3 163 T D A L H V Y S T 3 165 A L HV Y S T V E 3 170 S T V E G Y I A Y 3 173 E G Y I A Y R H D 3 178 Y R HD Q K G S C 3 186 C F I Q T L V D V 3 189 Q T L V D V F T K 3 191 L V DV F T K R K 3 192 V D V F T K R K G 3 196 T K R K G H I L E 3 203 L E LL T E V T R 3 207 T E V T R R M A E 3 208 E V T R R M A E A 3 213 M A EA E L V Q E 3 217 E L V Q E G K A R 3 220 Q E G K A R K T N 3 223 K A RK T N P E I 3 226 K T N P E I Q S T 3 229 P E I Q S T L R K 3 230 E I QS T L R K R 3 232 Q S T L R K R L Y 3 7 L E E E K Y D M S 2 9 E E K Y DM S G A 2 24 C V T K A R E G S 2 32 S E E D L D A L E 2 33 E E D L D A LE H 2 41 H M F R Q L R F E 2 49 E S T M K R D P T 2 61 F Q E E L E K F Q2 62 Q E E L E K F Q Q 2 63 E E L E K F Q Q A 2 66 E K F Q Q A I D S 267 K F Q Q A I D S R 2 68 F Q Q A I D S R E 2 70 Q A I D S R E D P 2 76E D P V S C A F V 2 77 D P V S C A F V V 2 80 S C A F V V L M A 2 81 C AF V V L M A H 2 82 A F V V L M A H G 2 84 V V L M A H C R E 2 89 H G R EG F L K G 2 91 R E G F L K G E D 2 109 F E A L N N K N C 2 114 N K N C QA L R A 2 118 Q A L R A K P K V 2 123 K P K V Y I I Q A 2 124 P K V Y IT Q A C 2 126 V Y I I Q A C R G 2 132 C R G E Q R D P G 2 138 D P G E TV G G D 2 146 D E I V M V I L K D 2 147 E I V M V I K D S 2 150 M V I KD S P Q T 2 156 P Q T I P T Y T D 2 157 Q T I P T Y T D A 2 159 I P T YT D A L H 2 169 Y S T V E G Y I A 2 172 V E G Y I A Y R H 2 174 G Y I AY R H D Q 2 175 Y I A Y R H D Q K 2 176 I A Y R H D Q K G 2 180 H D Q KG S C F I 2 185 S C F I Q T L V D 2 190 T L V D V F T K R 2 194 V F T KR K G H I 2 201 H I L E L L T E V 2 215 E A E L V Q E G K 2 221 E G K AR K T N P 2 222 G K A R K T N P E 2 224 A R K T N P E I Q 2 234 T L R KR L Y L Q 2 2 S N P R S L E E E 1 3 N P R S L E E E K 1 4 P R S L E E EK Y 1 5 R S L E E E K Y D 1 16 G A R L A L I L C 1 17 A R L A L I L C V1 20 A L I L C V T K A 1 21 L I L C V T K A R 1 36 L D A L E H M F R 139 L E H M F R Q L R 1 46 L R F E S T M K R 1 92 E G F L K G E D G 1 95L K G E D G E M V 1 106 E N L F E A L N N 1 107 N L F E A L N N K 1 108L F E A L N N K N 1 116 N C Q A L R A K P 1 117 C Q A L R A K P K 1 122A K P K V Y I I Q 1 139 P G E T V G G D E 1 155 S P Q T I P T Y T 1 164D A L H V Y S T V 1 167 H V Y S T V E G Y 1 168 V Y S T V E G Y I 1 181D Q K G S C F I Q 1 184 G S C F I Q T L V 1 193 D V F T K R K G H 1 209V T R R M A E A E 1 216 A E L V Q E G K A 1 225 R K T N P E I Q S 1 228N P E I Q S T L R 1 213P1F11 v.1: HLA-B*2705 nonamers 197 K R K G H I LE L 29 46 L R F E S T M K R 28 53 K R D P T A E Q F 25 28 A R E G S E ED L 24 4 P R S L E E E K Y 22 210 T R R M A E A E L 22 120 L R A K P K VY I 21 97 G E D G E M V K L 19 17 A R L A L I L C V 18 59 E Q F Q E E LE K 18 67 K F Q Q A I D S R 18 107 N L F E A L N N K 18 125 K V Y I I QA C R 18 179 R H D Q K G S C F 18 204 E L L T E V T R R 18 229 P E I Q ST L R K 18 75 R E D P V S C A F 17 100 G E M V K L E N L 17 218 L V Q EG K A R K 17 11 K Y D M S G A R L 16 44 R Q L R F E S T M 16 90 G R E GF L K G E 16 96 K G E D G E M V K 16 136 Q R D P G E T V G 16 171 T V EG Y I A Y R 16 183 K G S C F I Q T I A 16 190 T L V D V F T K R 16 198 RK C H I L E L L 16 211 R R M A E A E L V 16 227 T N P E I Q S T L 16 19L A L T L C V T K 15 31 G S E E D L D A L 15 40 E H M F R Q L R F 15 57T A E Q F Q E E L 15 60 Q F Q E E L E K F 15 101 E M V K L E N L F 15115 K N C Q A L R A K 15 145 G D E I V M V I K 15 203 L E L L T E V T R15 45 Q L R F E S T M K 14 81 C A F V V L M A H 14 121 R A K P K V Y I I14 144 G G D E I V M V I 14 189 Q T L V D V F T K 14 215 E A E L V Q E GK 14 217 E L V Q E G K A R 14 231 I Q S T L R K R L 14 233 S T L R K R LY L 14 10 E K Y D M S G A R 13 13 D M S G A R L A L 13 15 S G A R L A LI L 13 21 L I L C V T K A R 13 36 L D A L E H M F R 13 74 S R E D P V SC A 13 83 F V V L M A H G R 13 94 F L K G E D G E M 13 104 K L E N L F EA L 13 113 N N K N C Q A L R 13 170 S T V E G Y I A Y 13 172 V E G Y I AY R H 13 187 F I Q T L V D V F 13 223 K A R K T N P E I 13 151 V I K D SP Q T I 8 228 N P E I Q S T L R 13 230 E I Q S T L R K R 12 3 N P R S LE E E K 12 6 S L E E E K Y D M 12 33 E E D L D A L E H 12 38 A L E H M FR Q L 12 43 F R Q L R F E S T 12 78 L M A H G R E G F 12 86 M A H G R EG F L 12 87 M A H G R E G F L 12 88 A H G R E G F L K 12 112 L N N K N CQ A L 12 117 C Q A L R A K P K 12 129 I Q A C R G E Q R 12 140 G E T V GG D E I 12 142 T V G G D E I V M 12 178 Y R H D Q K G S C 12 191 L V D VF T K R K 12 193 D V F T K R K G H 12 205 L L T E V T R R M 12 34 E D LD A L E H M 11 35 D L D A L E H M F 11 119 A L R A K P K V Y 11 132 C RG E Q R D P G 11 159 I P T Y T D A L H 11 167 H V Y S T V E G Y 11 175 YI A Y R H D Q K 11 180 H D Q K G S C F I 11 195 F T K R K G H I L 11 224A R K T N P E I Q 11 39 L E H M F R Q L R 10 64 E L E K F Q Q A I 10 79V S C A F V V L M 10 158 T I P T Y T D A L 10 161 T Y T D A L V Y 10 200G H I L E L L T E 10 232 Q S T L R K R L Y 10 20 A L I L C V T K A 9 93G F L K G E D G E 9 194 V F T K R K G H I 9 5 R S L E E E K Y D 8 14 M SG A R L A L I 8 18 R L A L I L C V T 8 133 R G E Q R D P G E 8 137 R D PG E T V G G 8 151 V I K D S P Q T I 8 184 G S C F I Q T L V 8 201 H I LE L L T E V 8 226 K T N P E I Q S T 8 27 K A R E G S E E D 8 66 E K F QQ A I D S 7 91 R E G F L K G E D 7 106 E N L F E A L N N 7 123 K P K V YI I Q A 7 150 M V I K D S P Q T 7 168 V Y S T V E G Y I 7 212 R M A E AE L V Q 7 225 R K T N P E I Q S 7 16 G A R L A L I L C 6 47 R F E S T MK R D 6 89 H G R E G F L K G 6 118 Q A L R A K P K V 6 131 A C R G E Q RD P 6 141 E T V G G D E I V 6 146 D E I V M V I K D 6 152 I K D S P Q TI P 6 176 I A Y R H D Q K G 6 186 C F I Q T L V D V 6 219 V Q E G K A RK T 6 8 E E E K Y D M S G 5 22 I L C V T K A R E 5 29 R E G S E E D L D5 37 D A L E H M F R Q 5 50 S T M K R D P T A 5 63 E E L E K F Q Q A 568 F Q Q A I D S R E 5 72 I D S R E D P V S 5 92 E G F L K G E D G 5 103V K L E N L F E A 5 108 L F E A L N N K N 5 122 A K P K V Y I I Q 5 124P K V Y T I Q A C 5 126 V Y I I Q A C R G 5 143 V G G D E I V M V 5 147E I V M V I K D S 5 157 Q T I P T Y T D A 5 164 D A L H V Y S T V 5 165A L H V Y S T V E 5 174 G Y I A Y R H D Q 5 185 S C F I Q T L V D 5 188T Q T L V D V F T 5 196 T K R K G H I L E 5 214 A E A E L V Q E G 5 216A E L V Q E G K A 5 221 E G K A R K T N P 5 222 G K A R K T N P E 5 1 MS N P R S L E E 4 23 L C V T K A R E G 4 30 E G S E E D L D A 4 41 H M FR Q L R F E 4 42 M F R Q L R F E S 4 54 R D P T A E Q F Q 4 55 D P T A EQ F Q E 4 62 Q E E L E K F Q Q 4 82 A F V V L M A H G 4 84 V V L M A H GR E 4 99 D G E M V K L E N 4 102 M V K L E N L F E 4 109 F E A L N N K NC 4 110 E A L N N K N C Q 4 111 A L N N K N C Q A 4 114 N K N C Q A L RA 4 116 N C Q A L R A K P 4 127 Y I I Q A C R G E 4 130 Q A C R G E Q RD 4 134 G E Q R D P G E T 4 148 I V M V I K D S P 4 149 V M V I K D S PQ 4 153 K D S P Q T I P T 4 160 P T Y T D A L H V 4 163 T D A L H V Y ST 4 166 L H V Y S T V E G 4 192 V D V F T K R K G 4 199 K G H I L E L LT 4 202 I L E L L T E V T 4 213 M A E A E L V Q E 4 234 T L R K R L Y LQ 4 2 S N P R S L E E E 3 12 Y D M S G A R L A 3 26 T K A R E G S E E 332 S E E D L D A L E 3 52 M K R D P T A E Q 3 65 L E K F Q Q A L D 3 70Q A I D S R E D P 3 73 D S R E D P V S C 3 77 D P V S C A F V V 3 80 S CA F V V L M A 3 155 S P Q T I P T Y T 3 156 P Q T I P T Y T D 3 177 A YR H D Q K G S 3 181 D Q K G S C F I Q 3 220 Q E G K A R K T N 3 7 L E EE K Y D M S 2 24 C V T K A R E G S 2 51 T M K R D P T A E 2 56 P T A E QF Q E E 2 61 F Q E E L E K F Q 2 69 Q Q A I D S R E D 2 76 E D P V S C AF V 2 98 E D G E M V K L E 2 105 L E N L F E A L N 2 128 I I Q A C R G EQ 2 135 E Q R D P G E T V 2 138 D P G E T V G G D 2 162 Y T D A L H V YS 2 169 Y S T V E G Y I A 2 173 E G Y I A Y R H D 2 182 Q K G S C F I QT 2 207 T E V T R R M A E 2 208 E V T R R M A E A 2 9 E E K Y D M S G A1 25 V T K A R E G S E 1 48 F E S T M K R D P 1 49 E S T M K R D P T 158 A E Q F Q E E L E 1 71 A I D S R E D P V 1 85 V L M A H G R E G 1 95L K G E D G E M V 1 139 P G E T V G G D E 1 209 V T R R M A E A E 1213P1F11 v.1: HLA-B*2709 nonamers 53 K R D P T A E Q F 23 197 K R K G HI L E L 23 211 R R M A E A E L V 23 17 A R L A L I L C V 22 28 A R E G SE E D L 21 210 T R R M A E A E L 20 120 L R A K P K V Y I 19 121 R A K PK V Y I I 15 198 R K G H I L E L L 15 31 G S E E D L D A L 14 44 R Q L RF E S T M 14 97 G E D G E M V K L 14 100 G E M V K L E N L 14 11 K Y D MS G A R L 13 75 R E D P V S C A P 13 90 G R E G F L K G E 13 144 G G D EI V M V I 13 160 P T Y T D A L H V 13 233 S T L R K R L Y L 13 15 S G AR L A L I L 12 38 A L E H M F R Q L 12 46 L R F E S T M K R 12 104 K L EN L F E A L 12 140 G E T V G G D E I 12 179 R H D Q K G S C F 12 183 K GS C F I Q T L 12 184 G S C F T Q T L V 12 231 I Q S T L R K R L 12 13 DM S G A R L A L 11 74 S R E D P V S C A 11 77 D P V S C A F V V 11 78 PV S C A F V V L 11 118 Q A L R A K P K V 11 136 Q R D P G E T V G 11 223K A R K T N P E I 11 224 A R K T N P E I Q 11 227 T N P E I Q S T L 11 4P R S L E E E K Y 10 34 E D L D A L E H M 10 40 E H M F R Q L R F 10 43F R Q L R F E S T 10 57 T A E Q F Q E E L 10 71 A I D S R E D P V 10 79V S C A F V V L M 10 87 M A H G R E G F L 10 112 L N N K N C Q A L 10132 C R G E Q R D P G 10 158 T I P T Y T D A L 10 164 D A L H V Y S T V10 178 Y R H D Q K G S C 10 186 C F I Q T L V D V 10 195 F T K R K G H IL 10 201 H I L E L L T E V 10 205 L L T E V T R R M 10 6 S L E E E K Y DM 9 95 L K G E D G E M V 9 101 E M V K L E N L F 9 141 E T V G G D E I V9 142 T V G G D E T V M 9 143 V G G D E I V M V 9 187 F I Q T L V D V F9 194 V F T K R K G H I 9 14 M S G A R L A L I 8 35 D L D A L E H M F 860 Q F Q E E L E K F 8 64 E L E K F Q Q A I 8 76 E D P V S C A F V 8 86L M A H G R E G F 8 94 F L K G E D G E M 8 135 E Q R D P G E T V 8 151 VI K D S P Q T I 8 168 V Y S T V E G Y I 8 180 H D Q K G S C F I 8 5 R SL E E E K Y D 6 47 R F E S T M K R D 6 225 R K T N P E I Q S 6 18 R L AL I L C V T 5 29 R E G S E E D L D 5 93 G F L K G E D G E 5 106 E N L FE A L N N 5 125 K V Y I I Q A C R 5 133 R G E Q R D P G E 5 137 R D P CE T V G G 5 200 G H I L E L L T E 5 212 R M A E A E L V Q 5 54 R D P T AE Q F Q 4 91 R E G F L K G E D 4 134 G E Q R D P G E T 4 145 G D E I V MV I K 4 150 M V I K D S P Q T 4 167 H V Y S T V E G Y 4 172 V E G Y I AY R H 4 174 G Y I A Y R H D Q 4 189 Q T L V D V F T K 4 204 E L L T E VT R R 4 16 G A R L A L I L C 3 19 L A L I L C V T K 3 20 A L I L C V T KA 3 33 E E D L D A L E H 3 37 D A L E H M F R Q 3 59 E Q F Q E E L E K 363 E E L E K F Q Q A 3 66 E K F Q Q A I D S 3 84 V V L M A H G R E 3 107N L F E A L N N K 3 114 N K N C Q A L R A 3 123 K P K V Y I I Q A 3 126V Y I I Q A C R O 3 153 K D S P Q T I P T 3 176 I A Y R H D Q K G 3 185S C F I Q T L V D 3 188 I Q T L V D V F T 3 199 K G H I L E L L T 3 203L E L L T E V T R 3 216 A E L V Q E G K A 3 222 G K A R K T N P E 3 226K T N P E I Q S T 3 229 P E I Q S T L R K 3 1 M S N P R S L E E 2 10 E KY D M S G A R 2 12 Y D M S G A R L A 2 21 L I L C V T K A R 2 22 I L C VT K A R E 2 23 L C V T K A R E G 2 27 K A R E G S E E D 2 41 H M F R Q LR F E 2 55 D P T A E Q F Q E 2 67 K F Q Q A I D S R 2 68 F Q Q A I D S RE 2 72 I D S R E D P V S 2 73 D S R E D P V S C 2 80 S C A F V V L M A 281 C A F V V L M A H 2 82 A F V V L M A H G 2 83 F V V L M A H G R 2 92E G F L K G E D G 2 96 K G E D G E M V K 2 103 V K L E N L F E A 2 110 EA L N N K N C Q 2 111 A L N N K N C Q A 2 115 K N C Q A L R A K 2 124 PK V Y I I Q A C 2 129 I Q A C R G E Q R 2 146 D E I V M V I K D 2 148 IV M V I K D S P 2 152 I K D S P Q T I P 2 156 P Q T I P T Y T D 2 157 QT I P T Y T D A 2 159 I P T Y T D A L H 2 163 T D A L H V Y S T 2 166 LH V Y S T V E G 2 169 Y S T V E G Y I A 2 173 E G Y I A Y R H D 2 177 AY R H D Q K G S 2 182 Q K G S C F I Q T 2 193 D V F T K R K G H 2 213 MA E A E L V Q E 2 214 A E A E L V Q E G 2 3 N P R S L E E E K 1 9 E E KY D M S G A 1 24 C V T K A R E G S 1 30 E G S E E D L D A 1 49 E S T M KR D P T 1 50 S T M K R D P T A 1 51 T M K R D P T A E 1 58 A E Q F Q E EL E 1 62 Q E E L E K F Q Q 1 69 Q Q A I D S R E D 1 70 Q A I D S R E D P1 88 A H G R E G F L K 1 89 H G R E G F L K G 1 98 E D G E M V K L E 199 D G E M V K L E N 1 102 M V K L E N L F E 1 109 F E A L N N K N C I117 C Q A L R A K P K 1 119 A L R A K P K V Y 1 122 A K P K V Y I I Q 1127 Y I I Q A C R G E 1 128 I I Q A C R G E Q 1 130 Q A C R G E Q R D 1131 A C R G E Q R D P 1 138 D P G E T V G G D 1 147 E I V M V I K D S 1149 V M V I K D S P Q 1 154 D S P Q T I P T Y 1 155 S P Q T I P T Y T 1161 T Y T D A L H V Y 1 162 Y T D A L H V Y S 1 165 A L H V Y S T V E 1170 S T V E G Y I A Y 1 175 Y I A Y R H D Q K 1 190 T L V D V F T K R 1191 L V D V F T K R K 1 192 V D V F T K R K G 1 202 I L E L L T E V T 1207 T E V T R R M A E 1 208 E V T R R M A E A 1 209 V T R R M A E A E 1217 E L V Q E G K A R 1 218 L V Q E G K A R K 1 219 V Q E G K A R K T 1221 E G K A R K T N P 1 230 E I Q S T L R K R 1 232 Q S T L R K R L Y 1234 T L R K R L Y L Q 1 213P1F11 v.1: HLA-B*4402 nonamers 75 R E D P V SC A F 26 97 G E D G E M V K L 24 100 G E M V K L E N L 22 140 G E T V GG D E I 18 53 K R D P T A E Q F 17 119 A L R A K P K V Y 17 13 D M S G AR L A L 16 33 E E D L D A L E H 16 38 A L E H M F R Q L 16 146 D E I V MV I K D 16 183 K G S C F I Q T L 16 197 K R K G H I L E L 16 40 E H M FR Q L R F 15 63 E E L E K F Q Q A 15 104 K L E N L F E A L 15 154 D S PQ T I P T Y 15 158 T I P T Y T D A L 15 207 T E V T R R M A E 15 216 A EL V Q E G K A 15 229 P E I Q S T L R K 15 231 I Q S T L R K R L 15 233 ST L R K R L Y L 15 15 S G A R L A L I L 14 28 A R E G S E E D L 14 58 AE Q F Q E E L E 14 78 P V S C A F V V L 14 101 E M V K L E N L F 14 109F E A L N N K N C 14 161 T Y T D A L H V Y 14 170 S T V E G Y I A Y 14203 L E L L T E V T R 14 214 A E A E L V Q E G 14 220 Q E G K A R K T N14 232 Q S T L R K R L Y 14 4 P R S L E E E K Y 13 31 G S E E D L D A L13 32 S E E D L D A L E 13 48 F E S T M K R D P 13 112 L N N K N C Q A L13 187 F I Q T L V D V F 13 198 R I C G H I L E L L 13 227 T N P E I Q ST L 13 8 E E E K Y D M S G 12 9 E E K Y D M S G A 12 11 K Y D M S G A RL 12 35 D L D A L E H M F 12 39 L E H M F R Q L R 12 60 Q F Q E E L E KF 12 62 Q E E L E K F Q Q 12 64 E L E K F Q Q A I 12 87 M A H G R E G FL 12 105 L E N L F E A L N 12 121 R A K P K V Y I I 12 134 G E Q R D P GE T 12 144 G G D E I V M V I 12 172 V E G Y I A Y R E 12 195 F T K R K GH I L 12 14 M S G A R L A L I 11 29 R E G S E E D L D 11 86 L M A H G RE G F 11 151 V I K D S P Q T I 11 167 H V Y S T V E G Y 11 179 R H D Q KG S C F 11 7 L E E E K Y D M S 10 57 T A E Q F Q E E L 10 65 L E K F Q QA I D 10 91 R E G F L K G E D 10 168 V Y S T V E G Y I 10 210 T R R M AE A E L 10 20 A L I L C V T K A 9 120 L R A K P K V Y I 9 194 V F T K RK G H I 9 223 K A R K T N P E I 9 17 A R L A L I L C V 8 180 H D Q K G SC F I 8 147 E I V M V I K D S 7 153 K D S P Q T I P T 7 200 G H I L E LL T E 7 226 K T N P E I Q S T 7 21 L I L C V T K A R 6 66 E K F Q Q A ID S 6 98 E D G E M V K L E 6 110 E A L N N K N C Q 6 123 K P K V Y I I QA 6 124 P K V Y I I Q A C 6 157 Q T I P T Y T D A 6 185 S C F I Q T L VD 6 193 D V F T K R K G H 6 217 E L V Q E G K A R 6 224 A R K T N P E IQ 6 1 M S N P R S L E E 5 10 E K Y D M S G A R 5 34 E D L D A L E H M 541 H M F R Q L R F E 5 59 E Q F Q E E L E K 5 70 Q A I D S R E D P 5 71A I D S R E D P V 5 81 C A F V V L M A H 5 88 A H G R E G F L K 5 92 E GF L K G E D G 5 106 E N L F E A L N N 5 107 N L F E A L N N K 5 111 A LN N K N C Q A 5 115 K N C Q A L R A K 5 117 C Q A L R A K P K 5 122 A KP K V Y I I Q 5 131 A C R G E Q R D P 5 136 Q R D P G E T V G 5 143 V GG D E I V M V 5 174 G Y I A Y R H D Q 5 177 A Y R H D Q K G S 5 186 C FI Q T L V D V 5 204 E L L T E V T R R 5 230 E I Q S T L R K R 5 2 S N PR S L E E E 4 12 Y D M S G A R L A 4 16 G A R L A L I L C 4 18 R L A L IL C V T 4 30 E G S E E D L D A 4 46 L R F E S T M K R 4 50 S T M K R D PT A 4 51 T M K R D P T A E 4 67 K F Q Q A T D S R 4 90 G R E G F L K G E4 126 V Y I I Q A C R G 4 127 Y I I Q A C R G E 4 135 E Q R D P G E T V4 137 R D P G E T V G G 4 150 M V I K D S P Q T 4 155 S P Q T I P T Y T4 165 A L H V Y S T V E 4 171 T V E G Y I A Y R 4 191 L V D V F T K R K4 208 E V T R R M A E A 4 209 V T R R M A E A E 4 219 V Q E G K A R K T4 5 R S L E E E K Y D 3 19 L A L I L C V T K 3 23 L C V T K A R E G 3 43F R Q L R F E S T 3 44 R Q L R F E S T M 3 49 E S T M K R D P T 3 72 I DS R E D P V S 3 74 S R E D P V S C A 3 76 E D P V S C A F V 3 79 V S C AF V V L M 3 80 S C A F V V L M A 3 82 A F V V L M A H G 3 83 F V V L M AH G R 3 89 H G R E G F L K G 3 96 K G E D G E M V K 3 103 V K L E N L FE A 3 113 N N K N C Q A L R 3 114 N K N C Q A L R A 3 116 N C Q A L R AK P 3 118 Q A L R A K P K V 3 141 E T V G G D E I V 3 142 T V G G D E IV N 3 160 P T Y T D A L H V 3 173 E G Y I A Y R H D 3 182 Q K G S C F IQ T 3 189 Q T L V D V F T K 3 190 T L V D V F T K R 3 199 K G H I L E LL T 3 202 I L E L L T E V T 3 211 R R M A E A E L V 3 213 M A E A E L VQ E 3 215 E A E L V Q E G K 3 221 E G K A R K T N P 3 222 G K A R K T NP E 3 225 R K T N P E I Q S 3 234 T L R K R L Y L Q 3 47 R F E S T M K RD 2 52 M K R D P T A E Q 2 54 R D P T A E Q F Q 2 61 F Q E E L E K F Q 273 D S R E D P V S C 2 77 D P V S C A F V V 2 85 V L M A H G R E G 2 102M V K L E N L F E 2 108 L F E A L N N K N 2 125 K V Y I I Q A C R 2 129I Q A C R G E Q R 2 148 I V M V I K D S P 2 156 P Q T I P T Y T D 2 162Y T D A L H V Y S 2 163 T D A L H V Y S T 2 164 D A L H V Y S T V 2 166L H V Y S T V E G 2 175 Y I A Y R H D Q K 2 176 I A Y R H D Q K G 2 184G S C F I Q T L V 2 188 I Q T L V D V F T 2 192 V D V F T K R K G 2 196T K R K G H I L E 2 201 H I L E L L T E V 2 205 L L T E V T R R M 2 206L T E V T R R M A 2 212 R M A E A E L V Q 2 228 N P E I Q S T L R 2 3 NP R S L E E E K 1 6 S L E E E K Y D M 1 24 C V T K A R E G S 1 25 V T KA R E G S E 1 26 T K A R E G S E E 1 27 K A R E G S E E D 1 36 L D A L EH M F R 1 37 D A L E H M F R Q 1 42 M F R Q L R F E S 1 55 D P T A E Q FQ E 1 56 P T A E Q F Q E E 1 68 F Q Q A I D S R E 1 69 Q Q A I D S R E D1 84 V V L M A H G R E 1 93 G F L K G E D G E 1 94 F L K G E D G E M 199 D G E M V K L E N 1 128 I I Q A C R G E Q 1 130 Q A C R G E Q R D 1132 C R G E Q R D P G 1 133 R G E Q R D P G E 1 138 D P G E T V G G D 1139 P G E T V G G D E 1 145 G D E I V M V I K 1 152 I K D S P Q T I P 1159 I P T Y T D A L H 1 178 Y R H D Q K G S C 1 181 D Q K G S C F I Q 1213P1F11 v.1: HLA-B*5101 nonamers 164 D A L H V Y S T V 28 77 D P V S CA F V V 26 121 R A K P K V Y I I 23 144 G G D E I V M V I 23 223 K A R KT N P E I 23 118 Q A L R A K P K V 22 37 D A L E H M F R Q 19 138 D P GE T V G G D 19 87 M A H G R E G F L 18 143 V G G D E T V M V 18 176 I AY R H D Q K G 18 19 L A L I L C V T K 17 57 T A E Q F Q E E L 17 151 V IK D S P Q T I 16 160 P T Y T D A L H V 16 55 D P T A E Q F Q E 15 183 KG S C F I Q T L 15 15 S G A R L A L I L 14 81 C A F V V L M A H 14 120 LR A K P K V Y I 14 168 V Y S T V E G Y I 14 201 H I L E L L T E V 14 213M A E A E L V Q E 14 14 M S G A R L A L I 13 17 A R L A L I L C V 13 99D G E M V K L E N 13 110 E A L N N K N C Q 13 123 K P K V Y I I Q A 13155 S P Q T I P T Y T 13 159 I P T Y T D A L H 13 194 V F T K R K G H I13 13 D M S G A R L A L 12 16 G A R L A L I L C 12 27 K A R E G S E E D12 70 Q A I D S R E D P 12 89 H G R E G F L K G 12 95 L K G E D G E M V12 173 E G Y I A Y R H D 12 215 E A E L V Q E G K 12 227 T N P E I Q S TL 12 228 N P E I Q S T L R 12 3 N P R S L E E E K 11 64 E L E K F Q Q AI 11 78 P V S C A F V V L 11 130 Q A C R G E Q R D 11 135 E Q R D P G ET V 11 180 H D Q K G S C F I 11 186 C F I Q T L V D V 11 76 E D P V S CA F V 10 96 K G E D G E M V K 10 97 G E D G E M V K L 10 140 G E T V G GD E I 10 146 D E I V M V T K D 10 158 T I P T Y T D A L 10 211 R R M A EA E L V 10 233 S T L R K R L Y L 10 30 E G S E E D L D A 9 31 G S E E DL D A L 9 38 A L E H M F R Q L 9 112 L N N K N C Q A L 9 139 P G E T V GG D E 9 141 E T V G G D E I V 9 154 D S P Q T I P T Y 9 184 G S C F I QT L V 9 197 K R K G H I L E L 9 11 K Y D M S G A R L 8 28 A R E G S E ED L 8 46 L R F E S T M K R 8 71 A I D S R E D P V 8 73 D S R E D P V S C8 92 E G F L K G E D G 8 100 G E M V K L E N L 8 190 T L V D V F T K R 8193 D V F T K R K G H 8 195 F T K R K G H I L 8 203 L E L L T E V T R 8205 L L T E V T R R M 8 221 E G K A R K T N P 8 21 L I L C V T K A R 7104 K L E N L F E A L 7 108 L F E A L N N K N 7 119 A L R A K P K V Y 7167 H V Y S T V E G Y 7 187 F I Q T L V D V F 7 198 R K G H I L E L L 7199 K G H I L E L L T 7 204 E L L T E V T R R 7 210 T R R M A E A E L 7219 V Q E G K A R K T 7 10 E K Y D M S G A R 6 23 L C V T K A R E G 6 63E E L E K F Q Q A 6 98 E D G E M V K L E 6 103 V K L E N L F E A 6 107 NL F E A L N N K 6 133 R G E Q R D P G E 6 142 T V G G D E T V M 6 161 TY T D A L H V Y 6 181 D Q K G S C F I Q 6 189 Q T L V D V F T K 6 212 RH A E A E L V Q 6 5 R S L E E E K Y D 5 7 L E E E K Y D M S 5 20 A L I LC V T K A 5 34 E D L D A L E H H 5 35 D L D A L E H M F 5 60 Q F Q E E LE K F 5 72 I D S R E D P V S 5 79 V S C A F V V L M 5 80 S C A F V V L MA 5 122 A K P K V Y I I Q 5 165 A L H V Y S T V E 5 185 S C F I Q T L VD 5 188 I Q T L V D V F T 5 192 V D V F T K R K G 5 202 I L E L L T E VT 5 218 L V Q E G K A R K 5 230 E I Q S T L R K R 5 12 Y D M S G A R L A4 18 R L A L I L C V T 4 22 I L C V T K A R E 4 44 R Q L R F E S T M 448 F E S T M K R D P 4 61 F Q E E L E K F Q 4 84 V V L M A H G R E 4 106E N L F E A L N N 4 114 N K N C Q A L R A 4 116 N C Q A L R A K P 4 125K V Y I I Q A C R 4 136 Q R D P G E T V G 4 147 E I V M V I K D S 4 162Y T D A L H V Y S 4 166 L H V Y S T V E G 4 171 T V E G Y T A Y R 4 191L V D V F T K R K 4 200 G H I L E L L T E 4 206 L T E V T R R M A 4 214A E A E L V Q E G 4 216 A E L V Q E G K A 4 220 Q E G K A R K T N 4 2 SN P R S L E E E 3 41 H M F R Q L R F E 3 47 R F E S T M K R D 3 50 S T MK R D P T A 3 51 T M K R D P T A E 3 56 P T A E Q F Q E E 3 66 E K F Q QA T D S 3 68 F Q Q A I D S R E 3 74 S R E D P V S C A 3 83 F V V L M A HG R 3 85 V L M A H G R E G 3 90 G R E G F L K G E 3 93 G F L K G E D G E3 102 M V K L E N L F E 3 109 F E A L N N K N C 3 126 V Y I I Q A C R G3 127 Y I I Q A C R G E 3 128 I I Q A C R G E Q 3 137 R D P G E T V G G3 145 G D E I V M V I K 3 152 I K D S P Q T T P 3 163 T D A L H V Y S T3 170 S T V E G Y I A Y 3 172 V E G Y I A Y R H 3 178 Y R H D Q K G S C3 196 T K R K G H I L E 3 209 V T R R M A E A E 3 229 P E I Q S T L R K3 234 T L R K R L Y L Q 3 1 M S N P R S L E E 2 4 P R S L E E E K Y 2 6S L E E E K Y D M 2 8 E E E K Y D M S G 2 25 V T K A R E G S E 2 33 E ED L D A L E H 2 36 L D A L E H M F R 2 39 L E H M F R Q L R 2 40 E H M FR Q L R F 2 43 F R Q L R F E S T 2 52 M K R D P T A E Q 2 53 K R D P T AE Q F 2 54 R D P T A E Q F Q 2 59 E Q F Q E E L E K 2 65 L E K F Q Q A ID 2 75 R E D P V S C A F 2 86 L M A H G R E G F 2 94 F L K G E D G E M 2101 E M V K L E N L F 2 105 L E N L F E A L N 2 111 A L N N K N C Q A 2115 K N C Q A L R A K 2 117 C Q A L R A K P K 2 129 I Q A C R G E Q R 2131 A C R G E Q R D P 2 132 C R G E Q R D P G 2 148 I V M V I K D S P 2149 V M V I K D S P Q 2 150 M V I K D S P Q T 2 156 P Q T I P T Y T D 2157 Q T I P T Y T D A 2 169 Y S T V E G Y I A 2 174 G Y I A Y R H D Q 2175 Y I A Y R H D Q K 2 182 Q K G S C F I Q T 2 207 T E V T R R M A E 2222 G K A R K T N P E 2 224 A R K T N P E I Q 2 24 C V T K A R E G S 126 T K A R E G S E E 1 32 S E E D L D A L E 1 42 M F R Q L R F E S 1 45Q L R F E S T M K 1 49 E S T M K R D P T 1 67 K F Q Q A I D S R 1 69 Q QA I D S R E D 1 82 A F V V L M A H G 1 113 N N K N C Q A L R 1 124 P K VY I I Q A C 1 134 G E Q R D P G E T 1 153 K D S P Q T I P T 1 177     <TABLE XIXA, part 2: MHC Class 1 nonamer analysis of 2213P1F11 v.2 (aa1-230) 213P1F11 v.2: HLA-A*0201 nonamers 38 D M I R K AH A L 22 20 S E AP P NP P L 18 8 G P T P F QD P L 13 17 Y L P S E AP P N 13 45 A L S R PWW M C 13 10 T P F Q D PL Y L 12 35 S P T D M IR K A 12 1 H V Y S T VE GP 10 4 S T V E G PT P F 10 15 P L Y L P SE A P 10 27 P L W N S QD T S 1032 Q D T S P TD M I 10 39 M I R K A HA L S 10 44 H A L S R PW W M 10 51W M C S R RG K D 10 5 T V E G P TP F Q 9 13 Q D P L Y LP S E 8 16 L Y LP S EA P P 8 14 D P L Y L PS E A 7 37 T D M I R KA H A 7 52 M C S R R GKD I 7 54 S R R G K DT S W 7 29 W N S Q D TS P T 6 31 S Q D T S PT D M 641 R K A H A LS R P 6 42 K A H A L SR P W 6 2 V Y S T V EG P T 5 12 F QD P L YL P S 5 18 L P S E A PP N P 5 23 P P N P P LW N S 5 28 L W N S QDT S P 5 33 D T S P T DM I R 5 43 A H A L S RP W W 5 3 Y S T V E GP T P4 11 P F Q D P LY L P 4 21 E A P P N PP L W 4 22 A P P N P PL W N 4 30 NS Q D T SP T D 4 40 I R K A H AL S R 4 46 L S R P W WM C S 4 47 S R P WW MC S R 4 55 R R G K D IS W N 4 6 V E G P T PF Q D 3 24 P N P P L WN SQ 3 26 P P L W N SQ D T 3 50 W W M C S RR G K 2 53 C S R R G KD T S 2 9P T P F Q DP L Y 1 36 P T D M I RK A H 1 48 R P W W M CS R R 1 7 E G P TP FQ D P −2 19 P S E A P PN P P −2 49 P W W M C SR R G −2 213P1F11 v.2:HLA-A1 nonamers 9 P T P F Q D PL Y 25 12 F Q D P L Y LP S 21 36 P T D MI R KA H 17 19 P S E A P P NP P 15 5 T V E G P T PF Q 12 31 S Q D T S PTD M 12 4 S T V E G P TP F 10 33 D T S P T D MI R 10 20 S E A P P N PP L8 22 A P P N P P LW N 8 34 T S P T D M IR K 8 46 L S R P W W MC S 8 3 YS T V E G PT P 7 54 S R R G K D IS W 7 10 T P F Q D P LY L 6 21 E A P PN P PL W 6 40 I R K A H A LS R 6 53 C S R R G K DI S 6 6 V E G P T P FQD 5 23 P P N P P L WN S 5 7 E G P T P F QD P 4 8 G P T P F Q DP L 4 16 LY L P S E AP P 4 24 P N P P L W NS Q 4 30 N S Q D T S PT D 4 35 S P T DM I RK A 4 45 A L S R P W WM C 4 2 V Y S T V E GP T 3 11 P F Q D P L YLP 3 17 Y L P S E A PP N 3 51 W M C S R R GK D 3 15 P L Y L P S EA P 2 28L W N S Q D TS P 2 32 Q D T S P T DM I 2 39 M I R K A H AL S 2 43 A H AL S R PW W 2 47 S R P W W M CS R 2 1 H V Y S T V EG P 1 13 Q D P L Y LPS E 1 25 N P P L W N SQ D 1 27 P L W N S Q DT S 1 50 W W H C S R RG K 152 M C S R R G KD I 1 213P1F11 v.2: HLA-A26 nonamers 9 P T P F Q D P L Y23 4 S T V E G P T P F 22 33 D T S P T D M I R 19 38 D M I R K A H A L18 1 H V Y S T V E G P 16 5 T V E G P T P F Q 13 56 R G K D I S W N F 137 E G P T P F Q D P 12 20 S E A P P N P P L 12 36 P T D M I R K A H 1239 M I R K A H A L S 12 10 T P F Q D P L Y L 11 11 P F Q D P L Y L P 1117 Y L P S E A P P N 11 8 G P T P F Q D P L 10 21 E A P P N P P L W 1031 S Q D T S P T D M 10 14 D P L Y L P S E A 9 15 P L Y L P S E A P 9 27P L W N S Q D T S 9 44 H A L S R P W W M 9 45 A L S R P W W M C 9 12 F QD P L Y L P S 8 13 Q D P L Y L P S E 7 23 P P N P P L W N S 7 41 R K A HA L S R P 7 34 T S P T D M I R K 6 35 S P T D M I R K A 6 47 S R P W W MC S R 6 55 R R G K D I S W N 6 24 P N P P L W N S Q 5 16 L Y L P S E A PP 4 18 L P S E A P P N P 4 54 S R R G K D I S W 4 6 V E G P T P F Q D 325 N P P L W N S Q D 3 28 L W N S Q D T S P 3 43 A H A L S R P W W 3 46L S R P W W M C S 3 29 W N S Q D T S P T 2 30 N S Q D T S P T D 2 32 Q DT S P T D M I 2 37 T D M I R K A H A 2 40 I R K A H A L S R 2 48 R P W WM C S R R 2 50 W W M C S R R G K 2 51 W M C S R R G K D 2 3 Y S T V E GP T P 1 22 A P P N P P L W N 1 26 P P L W N S Q D T 1 42 K A H A L S R PW 1 49 P W W M C S R R G 1 213P1F11 v.2: HLA-A3 nonamers 40 I R KA H ALS R 17 45 A L SR P W WM C 17 15 P L YL P S EA P 16 27 P L WN S Q DT S15 1 H V YS T V EG P 14 39 M I RK A H AL S 14 17 Y L PS E A PP N 13 5 TV EG P T PF Q 12 38 D M IR K A HA L 11 48 R P WW M C SR R 11 50 W W MC SR RG K 11 4 S T VE G P TP F 10 34 T S PT D M IR K 10 56 R G KD I S WN F10 22 A P PN P P LW N 9 54 S R RG K D IS W 9 16 L Y LP S E AP P 8 33 D TSP T D MI R 8 41 R K AH A L SR P 8 52 M C SR R G KD I 8 53 C S RR G K DIS 8 55 R R GK D I SW N 8 3 Y S TV E G PT P 7 6 V E GP T P FQ D 7 25 N PPL W N SQ D 7 43 A H AL S R PW W 7 46 L S RP W W MC S 7 47 S R PW W M CSR 7 9 P T PF Q D PL Y 6 12 F Q DP L Y LP S 6 14 D P LY L P SE A 6 36 P TDM I R KA H 6 37 T D MI R K AH A 6 44 H A LS R P WW M 6 13 Q D PL Y L PSE 5 20 S E AP P N PP L 5 24 P N PP L W NS Q 5 30 N S QD T S PT D 5 42 KA HA L S RP W 5 10 T P FQ D P LY L 4 21 E A PP N P PL W 4 51 W M CS R RGK D 4 8 G P TP F Q DP L 3 19 P S EA P P NP P 3 23 P P NP P L WN S 3 28L W NS Q D TS P 3 29 W N SQ D T SP T 3 31 S Q DT S P TD M 3 32 Q D TS PT DM I 3 2 V Y ST V E GP T 2 18 L P SE A P PN P 2 26 P P LW N S QD T 235 S P TD M I RK A 2 11 P F QD P L YL P 1 213P1F11 v.2: HLA-B*0702nonamers 8 G P T P F Q D P L 22 10 T P F Q D P L Y L 22 20 S E A P P N PP L 17 22 A P P N P P L W N 17 14 D P L Y L P S E A 16 26 P P L W N S QD T 16 35 S P T D M I R K A 16 23 P P N P P L W N S 14 18 L P S E A P PN P 13 38 D M I R K A H A L 11 48 R P W W M C S R R 11 25 N P P L W N SQ D 10 29 W N S Q D T S P T 10 32 Q D T S P T D M I 10 2 V Y S T V E G PT 9 52 M C S R R G K D I 9 4 S T V E C P T P F 8 5 T V E G P T P F Q 831 S Q D T S P T D M 8 37 T D M I R K A H A 8 45 A L S R P W W M C 7 56R G K D I S W N F 7 44 H A L S R P W W M 6 7 E G P T P F Q D P 5 12 F QD P L Y L P S 5 19 P S E A P P N P P 5 43 A H A L S R P W W 5 15 P L Y LP S E A P 4 39 M I R K A H A L S 4 40 I R K A H A L S R 4 54 S R R G K DI S W 4 11 P F Q D P L Y L P 3 16 L Y L P S E A P P 3 21 E A P P N P P LW 3 33 D T S P T D M I R 3 36 P T D M I R K A H 3 42 K A H A L S R P W 346 L S R P W W M C S 3 55 R R G K D I S W N 3 3 Y S T V E G P T P 2 6 VE G P T P F Q D 2 17 Y L P S E A P P N 2 41 R K A H A L S R P 2 50 W W MC S R R G K 2 53 C S R R G K D I S 2 1 H V Y S T V E G P 1 9 P T P F Q DP L Y 1 13 Q D P L Y L P S E 1 24 P N P P L W N S Q 1 28 L W N S Q D T SP 1 30 N S Q D T S P T D 1 51 W M C S R R G K D 1 213P1F11 v.2: HLA-B*08nonamers 38 D M I R K A H A L 21 54 S R R G K D T S W 18 8 G P T P F Q DP L 17 10 T P F Q D P L Y L 16 56 R G K D I S W N F 16 52 M C S R R G KD I 15 20 S E A P P N P P L 13 44 H A L S R P W W M 13 40 I R K A H A LS R 11 4 S T V E G P T P F 10 39 M I R K A H A L S 10 35 S P T D M I R KA 9 14 D P L Y L P S E A 8 15 P L Y L P S E A P 8 18 L P S E A P P N P 825 N P P L W N S Q D 8 37 T D M I R K A H A 8 51 W M C S R R G K D 8 17Y L P S E A P P N 6 21 E A P P N P P L W 6 22 A P P N P P L W N 6 23 P PN P P L W N S 6 26 P P L W N S Q D T 6 27 P L W N S Q D T S 6 32 Q D T SP T D M I 6 45 A L S R P W W M C 6 46 L S R P W W M C S 6 48 R P W W M CS R R 6 53 C S R R G K D I S 6 42 K A H A L S R P W 4 1 H V Y S T V E GP 2 7 E G P T P F Q D P 2 31 S Q D T S P T D M 2 36 P T D M I R K A H 247 S R P W W M C S R 2 2 V Y S T V E G P T 1 3 Y S T V E G P T P 1 6 V EG P T P F Q D 1 12 F Q D P L Y L P S 1 13 Q D P L Y L P S E 1 43 A H A LS R P W W 1 55 R R G K D I S W N 1 213P1F11 v.2: HLA-B*1510 nonamers 20S E A P P N P P L 15 8 G P T P F Q D P L 13 10 T P F Q D P L Y L 13 43 AH A L S R P W W 13 38 D M I R K A H A L 11 4 S T V E G P T P F 9 31 S QD T S P T D M 7 44 H A L S R P W W M 7 56 R G K D I S W N F 7 21 E A P PH P P L W 6 5 T V E G P T P F Q 5 3 Y S T V E G P T P 4 18 L P S E A P PN P 4 34 T S P T D M I R K 4 35 S P T D M I R K A 4 49 P W W M C S R R G4 6 V E G P T P F Q D 3 19 P S E A P P N P P 3 23 P P N P P L W N S 3 30N S Q D T S P T D 3 33 D T S P T D M I R 3 41 R K A H A L S R P 3 50 W WM C S R R G K 3 7 E G P T P F Q D P 2 11 P F Q D P L Y L P 2 12 F Q D PL Y L P S 2 14 D P L Y L P S E A 2 15 P L Y L P S E A P 2 16 L Y L P S EA P P 2 17 Y L P S E A P P N 2 22 A P P N P P L W N 2 24 P N P P L W N SQ 2 29 W N S Q D T S P T 2 36 P T D M I R K A H 2 37 T D M I R K A H A 240 I R K A H A L S R 2 42 K A H A L S R P W 2 45 A L S R P W W M C 2 46L S R P W W M C S 2 48 R P W W M C S R R 2 53 C S R R G K D I S 2 55 R RG K D I S W N 2 1 H V Y S T V E G P 1 2 V Y S T V E G P T 1 9 P T P F QD P L Y 1 13 Q D P L Y L P S E 1 26 P P L W N S Q D T 1 27 P L W N S Q DT S 1 32 Q D T S P T D M I 1 39 M I R K A H A L S 1 47 S R P W W M C S R1 51 W M C S R R G K D 1 52 M C S R R G K D I 1 54 S R R G K D I S W 1213P1F11 v.2: HLA-B*2705 nonamers 40 I R K A H A L S R 24 47 S R P W W MC S R 21 55 R R G K D I S W N 20 56 R G K D I S W N F 19 48 R P W W M CS R R 17 4 S T V E G P T P F 16 8 G P T P F Q D P L 16 10 T P F Q D P LY L 16 54 S R R G K D I S W 16 20 S E A P P N P P L 14 38 D M I R K A HA L 14 33 D T S P T D M I R 13 34 T S P T D M I R K 13 31 S Q D T S P TD M 11 44 H A L S R P W W M 11 50 W W M C S R R G K 11 9 P T P F Q D P LY 10 36 P T D M I R K A H 9 41 R K A H A L S R P 8 32 Q D T S P T D M I7 23 P P N P P L W N S 6 52 M C S R R G K D I 6 14 D P L Y L P S E A 515 P L Y L P S E A P 5 16 L Y L P S E A P P 5 35 S P T D M I R K A 5 5 TV E G P T P F Q 4 13 Q D P L Y L P S E 4 18 L P S E A P P N P 4 24 P N PP L W N S Q 4 25 N P P L W N S Q D 4 27 P L W N S Q D T S 4 28 L W N S QD T S P 4 42 K A H A L S R P W 4 43 A H A L S R P W W 4 1 H V Y S T V EG P 3 3 Y S T V E G P T P 3 11 P F Q D P L Y L P 3 12 F Q D P L Y L P S3 17 Y L P S E A P P N 3 22 A P P N P P L W N 3 26 P P L W N S Q D T 329 W N S Q D T S P T 3 30 N S Q D T S P T D 3 39 M I R K A H A L S 3 45A L S R P W W M C 3 49 P W W M C S R R G 3 53 C S R R G K D I S 3 6 V EG P T P F Q D 2 19 P S E A P P N P P 2 21 E A P P N P P L W 2 37 T D M IR K A H A 2 46 L S R P W W M C S 2 51 W M C S R R G K D 2 2 V Y S T V EG P T 1 7 E G P T P F Q D P 1 213P1F11 v.2: HLA-B*2709 nonamers 8 G P TP F Q D P L 15 55 R R G K D I S W N 15 10 T P F Q D P L Y L 14 56 R G KD I S W N F 14 40 I R K A H A L S R 13 20 S E A P P N P P L 12 38 D M IR K A H A L 12 44 H A L S R P W W M 11 32 Q D T S P T D M I 10 47 S R PW W M C S R 10 54 S R R G K D I S W 10 4 S T V E G P T P F 9 31 S Q D TS P T D M 8 52 M C S R R G K D I 8 41 R K A H A L S R P 5 48 R P W W M CS R R 5 1 H V Y S T V E G P 4 16 L Y L P S E A P P 3 17 Y L P S E A P PN 3 3 Y S T V E G P T P 2 6 V E G P T P F Q D 2 12 F Q D P L Y L P S 214 D P L Y L P S E A 2 15 P L Y L P S E A P 2 18 L P S E A P P N P 2 21E A P P N P P L W 2 22 A P P N P P L W N 2 23 P P N P P L W N S 2 2 P PL W N S Q D T 2 34 T S P T D M I R K 2 42 K A H A L S R P W 2 43 A H A LS R P W W 2 5 T V E G P T P F Q 1 9 P T P F Q D P L Y 1 11 P F Q D P L YL P 1 13 Q D P L Y L P S E 1 24 P I I P P L W N S Q 1 25 N P P L W N S QD 1 28 L W N S Q D T S P 1 29 W N S Q D T S P T 1 3 N S Q D T S P T D 133 D T S P T D M I R 1 35 S P T D M I R K A 1 3 P T D M I R K A H 1 45 AL S R P W W M C 1 4 L S R P W W M C S 1 49 P W W M C S R R G 1 51 W M CS R R G K D 1 213P1F11 v.2: HLA-B*4402 nonamers 20 S E A P P N P P L 2421 E A P P N P P L W 19 38 D M I R K A H A L 18 6 V E G P T P F Q D 1543 A H A L S R P W W 15 10 T P F Q D P L Y L 14 8 G P T P F Q D P L 1352 M C S R R G K D I 13 54 S R R G K D I S W 13 4 S T V E G P T P F 12 9P T P F Q D P L Y 12 42 K A H A L S R P W 12 56 R G K D I S W N F 12 32Q D T S P T D M I 9 22 A P P N P P L W N 7 35 S P T D M I R K A 7 36 P TD M I R K A H 7 7 E G P T P F Q D P 5 12 F Q D P L Y L P S 5 24 P N P PL W N S Q 5 45 A L S R P W W M C 5 16 L Y L P S E A P P 4 23 P P N P P LW N S 4 25 N P P L W N S Q D 4 31 S Q D T S P T D H 4 33 D T S P T D M IR 4 11 P F Q D P L Y L P 3 13 Q D P L Y L P S E 3 15 P L Y L P S E A P 330 N S Q D T S P T D 3 34 T S P T D M I R K 3 44 H A L S R P W W M 3 46L S R P W W M C S 3 50 W W M C S R R G K 3 51 W M C S R R G K D 3 55 R RG K D T S W N 3 2 V Y S T V E G P T 2 5 T V E G P T P F Q 2 14 D P L Y LP S E A 2 17 Y L P S E A P P N 2 18 L P S E A P P N P 2 19 P S E A P P NP P 2 26 P P L W N S Q D T 2 27 P L W N S Q D T S 2 29 W N S Q D T S P T2 37 T D M I R K A H A 2 40 I R K A H A L S R 2 47 S R P W W M C S R 2 1H V Y S T V E G P 1 3 Y S T V E G P T P 1 39 M I R K A H A L S 1 41 R KA H A L S R P 1 49 P W W M C S R R G 1 53 C S R R G K D I S 1 213P1F11v.2: HLA-B *5101 nonamers 10 T P F Q D P L Y L 20 14 D P L Y L P S E A17 8 G P T P F Q D P L 16 35 S P T D M I R K A 16 18 L P S E A P P N P15 22 A P P N P P L W N 13 25 N P P L W N S Q D 13 44 H A L S R P W W M13 48 R P W W M C S R R 13 21 E A P P N P P L W 12 26 P P L W N S Q D T12 38 D M I R K A H A L 12 42 K A H A L S R P W 12 52 M C S R R G K D I12 23 P P N P P L W N S 11 32 Q D T S P T D M I 10 7 E G P T P F Q D P 91 H V Y S T V E G P 7 20 S E A P P N P P L 7 56 R G K D I S W N F 7 16 LY L P S E A P P 5 30 N S Q D T S P T D 5 33 D T S P T D M I R 5 34 T S PT D M T R K 5 40 I R K A H A L S R 5 2 V Y S T V E G P T 4 3 Y S T V E GP T P 4 4 S T V E G P T P F 4 15 P L Y L P S E A P 4 17 Y L P S E A P PN 4 27 P L W M S Q D T S 4 31 S Q D T S P T D M 4 6 V E G P T P F Q D 313 Q D P L Y L P S E 3 19 P S E A P P N P P 3 28 L W H S Q D T S P 3 49P W W M C S R R G 3 54 S R R G K D I S W 3 5 T V E G P T P F Q </t TABLEXIXA, part 3: MHC Class I nonamer analysis of 213P1F11 v.3(aa1-146)213P1F11 v.3: HLA-A*0201 nonamers 10 T L P S P F P Y L 22 3 I Q A C R GA T L 18 1 Y I I Q A C R G A 17 9 A T L P S P F P Y 10 12 P S P F P Y LS L 10 5 A C R G A T L P S 7 6 C R G A T L P S P 7 4 Q A C R G A T L P 68 G A T L P S P F P 6 11 L P S P F P Y L S 6 7 R G A T L P S P F 3213P1F11 v.3: HLA-A1 nonamers 9 A T L P S P F P Y 26 12 P S P F P Y L SL 11 5 A C R G A T L P S 8 11 L P S P F P Y L S 6 10 T L P S P F P Y L 54 Q A C R G A T L P 4 1 Y T I Q A C R G A 2 2 I I Q A C R G A T 1 3 I QA C R G A T L 1 8 G A T L P S P F P 1 213P1F11 v.3: HLA-A26 nonamers 9 AT L P S P F P Y 23 10 T L P F P Y L 23 1 Y I I Q A C R G A 14 12 P S P FP Y L S L 14 7 R G A T L P S P F 13 2 I I Q A C R G A T 11 3 I Q A C R GA T L 10 6 C R G A T L P S P 6 5 A C R G A T L P S 2 11 L P S P F P Y LS 2 8 G A T L P S P F P 1 213P1F11v.3: HLA-A3 nonamers 2 I I QA C R G AT 15 3 I Q AC R G A T L 15 9 A T LP S P F P Y 15 7 R G AT L P S P F 13 1Y I IQ A C R G A 11 4 Q A CR G A T L P 11 5 A C RG A T L P S 11 10 T LPS P F P Y L 10 12 P S PF P Y L S L 5 6 C R GA T L P S P 4 11 L P SP F PY L 2 4 8 G A TL P S P F P 1 213P1F11 v.3: HLA-B*0702 nonamers 10 T L PS P F P Y L 15 12 P S P F P Y L S L 15 3 I Q A C R G A T L 14 11 L P S PF P Y L S 13 2 I I Q A C R G A T 10 5 A C R G A T L P S 10 7 R G A T L PS P F 9 1 Y I I Q A C R G A 6 8 G A T L P S P F P 5 9 A T L P S P F P Y4 6 C R G A T L P S P 3 4 Q A C R G A T L P 1 213P1F11 v.3: HLA-B*08nonamers 3 I Q A C R G A T L 19 10 T L P S P F P Y L 16 12 P S P F P Y LS L 10 2 I I Q A C R G A T 6 5 A C R G A T L P S 6 7 R G A T L P S P F 68 G A T L P S P F P 6 11 L P S P F P Y L S 6 1 Y I I Q A C R G A 4 4 Q AC R G A T L P 4 213P1F11 v.3: HLA-B*1510 nonamers 3 I Q A C R G A T L 1410 T L P S P F P Y L 13 12 P S P F P Y L S L 11 7 R G A T L P S P F 8 1Y I I Q A C R G A 4 2 I I Q A C R G A T 4 11 L P S P F P Y L S 4 8 G A TL P S P F P 3 9 A T L P S P F P Y 3 4 Q A C R G A T L P 1 5 A C R G A TL P S 1 6 C R G A T L P S P 1 213P1F11 v.3: HLA-B*2705 nonamers 7 R G AT L P S P F 16 3 I Q A C R G A T L 13 6 C R G A T L P S P 13 9 A T L P SP F P Y 13 12 P S P F P Y L S L 13 10 T L P S P F P Y L 12 8 G A T L P SP F P 7 4 Q A C R G A T L P 5 1 Y I I Q A C R G A 4 5 A C R G A T L P S4 11 L P S P F P Y L S 2 2 I I Q A C R G A T 1 213P1F11 v.3: HLA-B*2709nonamers 7 R G A T L P S P F 12 10 T L P S P F P Y L 12 3 I Q A C R G AT L 11 6 C R G A T L P S P 11 12 P S P F P Y L S L 11 8 G A T L P S P FP 5 9 A T L P S P F P Y 4 5 A C R G A T L P S 2 11 L P S P F P Y L S 2 1Y I I Q A C R G A 1 2 I I Q A C R G A T 1 4 Q A C R G A T L P 1 213P1F11v.3: HLA-B*4402 nonamers 9 A T L P S P F P Y 18 3 I Q A C R G A T L 12 7R G A T L P S P F 12 10 T L P S P F P Y L 12 12 P S P F P Y L S L 12 5 AC R G A T L P S 6 11 L P S P F P Y L S 6 1 Y I I Q A C R G A 4 2 I I Q AC R G A T 3 4 Q A C R G A T L P 3 6 C R G A T L P S P 1 8 G A T L P S PF P 1 213P1F11 v.3: HLA-B*5101 nonamers 11 L P S P F P Y L S 13 4 Q A CR G A T L P 12 3 I Q A C R G A T L 10 8 G A T L P S P F P 10 10 T L P SP F P Y L 9 7 R G A T L P S P F 8 12 P S P F P Y L S L 8 9 A T L P S P FP Y 4 1 Y I I Q A C R G A 3 TABLE XIXA, part 4: MHC Class 1 nonameranalysis of 213P1F11 v.4 (aa 1-321) 213P1F11 v.4: HLA-A*0201 nonamers 68D I V G R DL S I 20 50 K L V N D PR E T 17 61 V F G G G VG D I 17 5 Q EY D K SL S V 16 3 K C Q E Y DK S L 15 13 V Q P E K RT G L 15 26 G E C GQ TF R L 15 33 R L K E E QG R A 15 75 S I S F R NS E T 15 10 S L S V QPE K R 14 20 G L R D E NG E C 14 39 G R A F R GS S V 14 53 N D P R E TQE V 14 46 S V H Q K LV N D 13 62 F G G G V GD I V 13 43 R G S S V HQ K L12 51 L V N D P RE T Q 11 58 T Q E V F GG G V 11 66 V G D I V GR D L 1112 S V Q P E KR T G 10 44 G S S V H QK L V 10 64 G G V G D IV G R 10 65G V G D I VG R D 10 69 I V G R D LS I S 10 60 E V F G G GV G D 9 73 D LS I S FR N S 9 30 Q T F R L KE E Q 8 74 L S I S F RN S E 8 77 S F R N SET S A 8 85 A S E E E KY D M 8 40 R A F R G SS V H 7 47 V H Q K L VN D P7 84 S A S E E EK Y D 7 9 K S L S V QP E K 6 11 L S V Q P EK R T 6 23 DE N G E CG Q T 6 41 A F R G S SV H Q 6 42 F R G S S VH Q K 6 79 R N S ET SA S E 6 17 K R T G L RD E N 5 67 G D I V G RD L S 5 70 V G R D L SI SF 5 71 G R D L S IS F R 5 76 I S F R N SE T S 5 78 F R N S E TS A S 5 7Y D K S L SV Q P 4 18 R T G L R DE N G 4 19 T G L R D EN G E 4 21 L R DE N GE C C 4 28 C G Q T F RL K E 4 29 G Q T F R LK E E 4 32 F R L K E EQG R 4 34 L K E E Q GR A F 4 35 K E E Q G RA F R 4 56 R E T Q E VF G G 457 E T Q E V FG G G 4 83 T S A S E EE K Y 4 86 S E E E K YD M S 4 2 G KC Q E YD K S 3 8 D K S L S VQ P E 3 16 E K R T G LR D E 3 38 Q G R A FRG S S 3 45 S S V H Q KL V N 3 49 Q K L V N DP R E 3 52 V N D P R ET Q E3 63 G G G V G DI V G 3 81 S E T S A SE E E 3 82 E T S A S EE E K 3 22 RD E N G EC G Q 2 72 R D L S I SF R N 2 6 E Y D K S LS V Q 1 14 Q P E K RTG L R 1 24 E N G E C GQ T F 1 25 N G E C G QT F R 1 31 T F R L K EE Q G1 54 D P R E T QE V F 1 59 Q E V F G GG V G 1 80 N S E T S AS E E 1 36 EE Q G R AF R G −1 48 H Q K L V ND P R −1 4 C Q E Y D KS L S −2 37 E Q GR A FR G S −2 55 P R E T Q EV F G −2 15 P E K R T GL R D −3 27 E C G Q TFR L K −3 213P1F11 v.4: HLA-A1 nonamers 83 T S A S E E EK Y 21 45 S S VH Q K LV N 15 52 V N D P R E TQ E 15 85 A S E E E K YD H 15 66 V G D I VG RD L 14 80 N S E T S A SE E 14 34 L K E E Q G RA F 13 35 K E E Q G RAF R 13 86 S E E E K Y DM S 13 4 C Q E Y D K SL S 12 14 Q P E K R T GL R12 22 R D E N G E CG Q 12 25 N G E C G Q TF R 12 55 P R E T Q E VF G 126 E Y D K S L SV Q 11 21 L R D E N G EC G 11 57 E T Q E V F GG G 11 58 TQ E V F G GG V 11 71 G R D L S I SF R 10 28 C G Q T F R LK E 9 10 S L SV Q P EK R 7 15 P E K R T G LR D 7 63 G G G V G D IV G 7 68 D I V G R DLS I 7 5 Q E Y D K S LS V 6 9 K S L S V Q PE K 6 12 S V Q P E K RT G 618 R T G L R D EN G 6 30 Q T F R L K EE Q 6 44 G S S V H Q KL V 6 82 E TS A S E EE K 6 11 L S V Q P E KR T 5 27 E C G Q T F RL K 5 61 V F G G GV GD I 5 62 F G G G V G DI V 5 67 G D I V G R DL S 5 70 V G R D L S IS F5 74 L S I S F R NS E 5 43 R G S S V H QK L 4 59 Q E V F G G GV G 4 60 EV F G G G VG D 4 73 D L S I S F RN S 4 76 I S F R N S ET S 4 26 G E C GQ T FR L 3 37 E Q G R A F RG S 3 40 R A F R G S SV H 3 48 H Q K L V N DPR 3 75 S I S F R N SE T 3 1 M G K C Q E YD K 2 2 G K C Q E Y DK S 2 7 YD K S L S VQ P 2 13 V Q P E K R TG L 2 16 E K R T G L RD E 2 17 K R T GL R DE N 2 20 G L R D E N GE C 2 41 A F R G S S VH Q 2 42 F R G S S V HQK 2 46 S V H Q K L VN D 2 47 V H Q K L V ND P 2 51 L V N D P R ET Q 2 77S F R N S E TS A 2 81 S E T S A S EE E 2 84 S A S E E E KY D 2 3 K C Q EY D KS L 1 8 D K S L S V QP E 1 23 D E N G E C GQ T 1 24 E N G E C G QTF 1 32 F R L K E E QG R 1 33 R L K E E Q GR A 1 36 E E Q G R A FR G 1 38Q G R A F R GS S 1 39 G R A F R G SS V 1 50 K L V N D P RE T 1 54 D P RE T Q EV F 1 56 R E T Q E V FG G 1 64 G G V G D I VG R 1 65 G V G D T VGR D 1 78 F R N S E T SA S 1 213P1F11 v.4: HLA-A26 nonamers 57 E T Q E VF G G G 23 60 E V F G G G V G D 22 73 D L S I S F R N S 20 24 E N G E CG Q T F 19 68 D I V G R D L S I 19 46 S V H Q K L V N D 18 54 D P R E TQ E V F 18 82 E T S A S E E E K 18 65 G V G D I V G R D 16 69 I V G R DL S I S 15 6 E Y D K S L S V Q 14 30 Q T F R L K E E Q 14 34 L K E E Q GR A F 14 13 V Q P E K R T G L 13 70 V G R D L S I S F 13 83 T S A S E EE K Y 13 8 D K S L S V Q P E 12 12 S V Q P E K R T G 12 26 G E C G Q T FR L 12 33 R L K E E Q G R A 12 61 V F G G G V G D I 12 75 S I S F R N SE T 12 3 K C Q E Y D K S L 11 18 R T C L R D E N C 11 27 E C G Q T F R LK 11 37 E Q G R A F R G S 11 41 A F R C S S V H Q 11 43 R G S S V H Q KL 11 51 L V N D P R E T Q 11 10 S L S V Q P E K R 10 16 E K R T G L H DE 10 20 G L R D E N G E C 10 85 A S E E E K Y D M 10 23 D E N G E C G QT 9 36 E E Q G R A F R G 9 50 K L V N D P R E T 9 66 V G D I V G R D L 931 T F R L K E E Q G 8 64 G G V C D I V G R 8 77 S F R N S E T S A 8 86S E E E K Y D M S 8 42 F R G S S V H Q K 7 71 G R D L S I S F R 7 2 G KC Q E Y D K S 6 47 V H Q K L V N D P 6 56 R E T Q E V F G G 6 7 Y D K SL S V Q P 5 29 G Q T F R L K E E 5 17 K R T G L R D E N 4 52 V N D P R ET Q E 4 74 L S I S F R N S E 4 79 R N S E T S A S E 4 5 Q E Y D K S L SV 3 9 K S L S V Q P E K 3 21 L R D E N G E C G 3 32 F R L K E E Q G R 339 G R A F R G S S V 3 40 R A F R G S S V H 3 53 N D P R E T Q E V 3 78F R N S E T S A S 3 80 N S E T S A S E E 3 1 M G K C Q E Y D K 2 11 L SV Q P E K R T 2 15 P E K R T G L R D 2 35 K E E Q G R A F R 2 49 Q K L VN D P R E 2 55 P R E T Q E V F G 2 62 F G G G V G D I V 2 67 G D I V G RD L S 2 72 R D L S I S F R N 2 76 I S F R N S E T S 2 81 S E T S A S E EE 2 84 S A S E E E K Y D 2 4 C Q E Y D K S L S 1 14 Q P E K R T G L R 119 T G L R D E N G E 1 22 R D E N G E C G Q 1 28 C G Q T F R L K E 1 38Q G R A F R G S S 1 45 S S V H Q K L V N 1 48 H Q K L V N D P R 1 58 T QE V F G G G V 1 213P1F11 v.4: HLA-A3 nonamers 60 E V FG G G VG D 21 40 RA FR G S SV H 20 12 S V QP E K RT G 18 69 I V GR D L ST S 18 33 R L KE EQ GR A 17 68 D I VG R D LS I 17 9 K S LS V Q PE K 16 10 S L SV Q P EK R16 46 S V HQ K L VN D 16 51 L V ND P R ET Q 16 20 G L RD E N GE C 15 50K L VN D P RE T 15 75 S I SF R N SE T 14 5 Q E YD K S LS V 13 213P1F11v.4: HLA-A3 nonamers 60 E V FG G G VG D 21 40 R A FR G S SV H 20 12 S VQP E K RT G 18 69 I V GR D L SI S 18 33 R L KE E Q GR A 17 68 D I VG R DLS I 17 9 K S LS V Q PE K 16 10 S L SV Q P EK R 16 46 S V HQ K L VN D 1651 L V ND P R ET Q 16 20 G L RD E N GE C 15 50 K L VN D P RE T 15 75 S ISF R N SE T 14 5 Q E YD K S LS V 13 35 K E EQ G R AF R 13 42 F R GS S VHQ K 13 24 E N GE C G QT F 12 41 A F RG S S VH Q 12 54 D P RE T Q EV F12 59 Q E VF G G GV G 12 65 G V GD I V GR D 12 82 E T SA S E EE K 12 1 MG KC Q E YD K 11 38 Q G RA F R GS S 11 39 G R AF R G SS V 11 73 D L SI SF RN S 11 15 P E KR T G LR D 10 27 E C GQ T F RL K 10 64 G G VG D I VG R10 70 V G RD L S IS F 10 79 R N SE T S AS E 10 14 Q P EK R T GL R 9 34 LK EE Q G RA F 9 52 V N DP R E TQ E 9 76 I S FR N S ET S 9 7 Y D KS L SVQ P 8 31 T F RL K E EQ G 8 45 S S VH Q K LV N 8 71 G R DL S I SF R 8 77S F RN S E TS A 8 6 E Y DK S L SV Q 7 18 R T GL R D EN G 7 22 R D EN G ECG Q 7 25 N G EC G Q TF R 7 36 E E QG R A FR G 7 48 H Q KL V N DP R 7 83T S AS E E EK Y 7 3 K C QE Y D KS L 6 17 K R TG L R DE N 6 23 D E NG E CGQ T 6 32 F R LK E E QG R 6 62 F G GG V G DI V 6 63 G G GV G D IV G 6 67G D IV G R DL S 6 72 R D LS I S FR N 6 74 L S IS F R NS E 6 80 N S ET SA SE E 6 16 E K RT G L RD E 5 19 T G LR D E NG E 5 30 Q T FR L K EE Q 543 R G SS V H QK L 5 61 V F GG G V GD I 5 66 V G DI V G RD L 5 13 V Q PEK R TG L 4 21 L R DE N G EC G 4 28 C G QT F R LK E 4 49 Q K LV N D PR E4 55 P R ET Q E VF G 4 56 R E TQ E V FG G 4 58 T Q EV F G GG V 4 78 F RNS E T SA S 4 85 A S EE E K YD M 4 86 S E EE K Y DM S 4 4 C Q EY D K SLS 3 37 E Q GR A F RG S 3 53 N D PR E T QE V 3 57 E T QE V F GG G 3 26 GE CG Q T FR L 2 29 G Q TF R L KE E 2 84 S A SE E E KY D 2 8 D K SL S VQP E 1 81 S E TS A S EE E 1 213P1F11 v.4: HLA-B*0702 nonamers 54 D P R ET Q E V F 19 26 G E C G Q T F R L 13 43 R G S S V H Q K L 13 13 V Q P EK R T G L 12 14 Q P E K R T G L R 12 66 V G D I V G R D L 12 3 K C Q E YD K S L 11 61 V F G G G V G D I 10 62 F G G G V G D I V 10 68 D I V G RD L S I 10 11 L S V Q P E K R T 9 24 E N G E C G Q T F 9 77 S F R N S ET S A 9 5 Q E Y D K S L S V 8 23 D E N G E C G Q T 8 34 L K E E Q G R AF 8 39 G R A F R G S S V 8 41 A F R G S S V H Q 8 44 G S S V H Q K L V 870 V G R D L S I S F 8 75 S I S F R N S E T 8 85 A S E E E K Y D M 8 33R L K E E Q G R A 7 50 K L V N D P R E T 7 53 N D P R E T Q E V 7 58 T QE V F G G G V 7 60 E V F G G G V G D 6 6 E Y D K S L S V Q 4 8 D K S L SV Q P E 4 17 K R T G L R D E N 4 35 K E E Q G R A F R 4 38 Q G R A F R GS S 4 51 L V N D P R E T Q 4 64 G G V G D T V G R 4 79 R N S E T S A S E4 82 E T S A S E E E K 4 15 P E K R T G L R D 3 16 E K R T G L R D E 327 E C G Q T F R L K 3 28 C G Q T F R L K E 3 36 E E Q G R A F R G 3 37E Q G R A F R G S 3 45 S S V H Q K L V N 3 52 V N D P R E T Q E 3 55 P RE T Q E V F G 3 73 D L S I S F R N S 3 7 Y D K S L S V Q P 2 9 K S L S VQ P E K 2 10 S L S V Q P E K R 2 18 R T G L R D E N G 2 20 G L R D E N GE C 2 21 L R D E N G E C G 2 25 N G E C G Q T F R 2 31 T F R L K E E Q G2 40 R A F R G S S V H 2 42 F R G S S V H Q K 2 46 S V H Q K L V N D 247 V H Q K L V N D P 2 56 R E T Q E V F G G 2 57 E T Q E V F G G G 2 59Q E V F G G G V G 2 63 G G G V G D I V G 2 65 G V G D I V G R D 2 69 I VG R D L S T S 2 71 G R D L S I S F R 2 78 F R N S E T S A S 2 84 S A S EE E K Y D 2 12 S V Q P E K R T G 1 22 R D E N G E C G Q 1 32 F R L K E EQ G R 1 48 H Q K L V N D P R 1 49 Q K L V N D P R E 1 67 G D I V G R D LS 1 72 R D L S I S F R N 1 74 L S I S F R N S E 1 76 I S F R N S E T S 183 T S A S E E E K Y 1 213P1F11 v.4: HLA-B*08 nonamers 13 V Q P E K R TG L 23 54 D P R E T Q E V F 20 33 R L K E E Q G R A 18 68 D I V G R D LS I 18 31 T F R L K E E Q G 17 75 S I S F R N S E T 16 20 G L R D E N GE C 15 14 Q P E K R T G L R 14 86 S E E E K Y D M S 14 3 K C Q E Y D K SL 13 46 S V H Q K L V N D 13 48 H Q K L V N D P R 13 70 V G R D L S I SF 13 7 Y D K S L S V Q P 11 26 G E C G Q T F R L 11 29 G Q T F R L K E E11 66 V G D I V G R D L 11 1 M G K C Q E Y D K 10 5 Q E Y D K S L S V 1015 P E K R T G L R D 10 24 E N G E C G Q T F 10 36 E E Q G R A F R G 1043 R G S S V H Q K L 10 10 S L S V Q P E K R 9 18 R T G L R D E N G 9 34L K E E Q G R A F 9 39 G R A F R G S S V 9 52 V H D P R E T Q E 9 84 S AS E E E K Y D 9 16 E K R T G L R D E 8 61 V F G G G V G D I 8 77 S F R NS E T S A 8 41 A F R G S S V H Q 7 50 K L V N D P R E T 7 38 Q G R A F RG S S 6 73 D L S I S F R N S 6 40 R A F R G S S V H 4 57 E T Q E V F G GG 4 44 G S S V H Q K L V 3 60 E V F G G G V G D 3 64 G G V G D I V G R 371 G R D L S I S F R 3 81 S E T S A S E E E 3 82 E T S A S E E E K 3 6 EY D K S L S V Q 2 8 D K S L S V Q P E 2 12 S V Q P E K R T G 2 21 L R DE N G E C G 2 27 E C G Q T F R L K 2 37 E Q G R A F R G S 2 42 F R G S SV H Q K 2 45 S S V H Q K L V N 2 47 V H Q K L V N D P 2 63 G G G V G D IV G 2 65 G V G D I V G R D 2 67 G D I V G R D L S 2 78 F R N S E T S A S2 79 R N S E T S A S E 2 85 A S E E E K Y D M 2 2 G K C Q E Y D K S 1 4C Q E Y D K S L S 1 9 K S L S V Q P E K 1 11 L S V Q P E K R T 1 17 K RT G L R D E N 1 30 Q T F R L K E E Q 1 32 F R L K E E Q G R 1 49 Q K L VN D P R E 1 53 N D P R E T Q E V 1 55 P R E T Q E V F G 1 56 R E T Q E VF G G 1 58 T Q E V F G G G V 1 62 F G G G V G D I V 1 69 I V G R D L S IS 1 76 I S F R N S E T S 1 80 N S E T S A S E E 1 213P1F11 v.4:HLA-B*1510 nonamers 26 G E C G Q T F R L 14 13 V Q P E K R T G L 12 47 VH Q K L V N D P 12 66 V G D I V G R D L 12 3 K C Q E Y D K S L 11 34 L KE E Q G R A F 11 43 R G S S V H Q K L 11 24 E N G E C G Q T F 9 54 D P RE T Q E V F 9 85 A S E E E K Y D M 9 70 V G R D L S I S F 7 12 S V Q P EK R T G 6 49 Q K L V N D P R E 5 60 E V F G G G V G D 5 63 G G G V G D TV G 5 64 G G V G D I V G R 5 65 G V G D I V G R D 5 6 E Y D K S L S V Q4 11 L S V Q P E K R T 4 16 E K R T G L R D E 4 27 E C G Q T F R L K 435 K E E Q G R A F R 4 36 E E Q G R A F R G 4 50 K L V N D P R E T 4 51L V N D P R E T Q 4 67 G D I V G R D L S 4 76 I S F R N S E T S 4 7 Y DK S L S V Q P 3 10 S L S V Q P E K R 3 17 K R T G L R D E N 3 20 G L R DE N G E C 3 33 R L K E E Q G R A 3 37 E Q G R A F R G S 3 40 R A F R G SS V H 3 41 A F R G S S V H Q 3 44 G S S V H Q K L V 3 45 S S V H Q K L VN 3 46 S V H Q K L V N D 3 55 P R E T Q E V F G 3 58 T Q E V F G G G V 359 Q E V F G G G V G 3 61 V F G G G V G D I 3 73 D L S I S F R N S 3 82E T S A S E E E K 3 2 G K C Q E Y D K S 2 4 C Q E Y D K S L S 2 8 D K SL S V Q P E 2 9 K S L S V Q P E K 2 14 Q P E K R T G L R 2 15 P E K R TG L R D 2 21 L R D E N G E C G 2 22 R D E N G E C G Q 2 25 N G E C G Q TF R 2 29 G Q T F R L K E E 2 30 Q T F R L K E E Q 2 39 G R A F R G S S V2 52 V N D P R E T Q E 2 56 R E T Q E V F G G 2 57 E T Q E V F G G G 269 I V G R D L S I S 2 71 G R D L S I S F R 2 72 R D L S I S F R N 2 75S I S F R N S E T 2 79 R N S E T S A S E 2 80 N S E T S A S E E 2 83 T SA S E E E K Y 2 84 S A S E E E K Y D 2 86 S E E E K Y D M S 2 5 Q E Y DK S L S V 1 19 T G L R D E N G E 1 23 D E N G E C G Q T 1 28 C G Q T F RL K E 1 31 T F R L K E E Q G 1 32 F R L K E E Q G R 1 38 Q G R A F R G SS 1 42 F R G S S V H Q K 1 53 N D P R E T Q E V 1 62 F G G G V G D I V 168 D I V G R D L S I 1 74 L S I S F R N S E 1 78 F R N S E T S A S 1 81S E T S A S E E E 1 213P1F11 v.4: HLA-B*2705 nonamers 71 G R D L S I S FR 29 32 F R L K E E Q G R 25 42 F R G S S V H Q K 23 40 R A F R G S S VH 20 64 G G V G D I V G R 20 9 K S L S V Q P E K 19 26 G E C G Q T F R L17 35 K E E Q G R A F R 17 43 R G S S V H Q K L 17 17 K R T G L R D E N16 25 N G E C G Q T F R 16 3 K C Q E Y D K S L 15 39 G R A F R G S S V15 13 V Q P E K R T G L 14 54 D P R E T Q E V F 14 70 V G R D L S 1S F14 48 H Q K L V N D P R 13 85 A S E E E K Y D M 13 10 S L S V Q P E K R12 14 Q P E K R T G L R 12 24 E N G E C G Q T F 12 27 E C G Q T F R L C12 68 D I V G R D L S I 12 78 F R N S E T S A S 12 82 E T S A S E E E K12 1 M G K C Q E Y D K 11 21 L R D E N G E C G 11 34 L K E E Q G R A F11 55 P R E T Q E V F G 11 61 V F G G G V G D I 11 66 V G D I V G R D L11 83 T S A S E E E K Y 11 33 R L K E E Q G R A 10 72 R D L S I S F R N10 2 G K C Q E Y D K S 8 18 R T G L R D E N G 8 56 R E T Q E V F G G 860 E V F G G G V G D 8 63 G G G V G D I V G 8 79 R N S E T S A S E 8 46S V H Q K L V N D 7 65 G V G D I V G R D 7 67 G D I V G R D L S 7 5 Q EY D K S L S V 6 6 E Y D K S L S V Q 6 11 L S V Q P E K R T 6 20 G L R DE N G E C 6 22 R D E N G E C G Q 6 30 Q T F R L K E E Q 6 41 A F R G S SV H Q 6 49 Q K L V N D P R E 6 76 I S F R K S E T S 6 29 G Q T F R L K EE 5 36 E E Q G R A F R G 5 44 G S S V H Q K L V 5 47 V H Q K L V N D P 57 Y D K S L S V Q P 4 12 S V Q P E K R T G 4 23 D E N G E C G Q T 4 45 SS V H Q K L V N 4 50 K L V N D P R E T 4 52 V N D P R E T Q E 4 59 Q E VF G G G V G 4 74 L S I S F R N S E 4 77 S F R N S E T S A 4 80 N S E T SA S E E 4 8 D K S L S V Q P E 3 15 P E K R T G L R D 3 16 E K R T G L RD E 3 19 T G L R D E N G E 3 28 C G Q T F R L K E 3 31 T F R L K E E Q G3 62 F G G G V G D I V 3 69 I V G R D L S I S 3 73 D L S I S F R N S 375 S I S F R N S E T 3 4 C Q E Y D K S L S 2 51 L V N D P R E T Q 2 53 ND P R E T Q E V 2 57 E T Q E V F G G G 2 81 S E T S A S E E E 2 84 S A SE E E K Y D 2 86 S E E E K Y D M S 2 38 Q G R A F R G S S 1 213P1F11v.4: HLA-B*2709 nonamers 39 G R A F R G S S V 21 43 R G S S V H Q K L 1526 G E C G Q T F R L 14 17 K R T G L R D E N 13 42 F R G S S V H Q K 1371 G R D L S I S F R 13 3 K C Q E Y D K S L 12 32 F R L K E E Q G R 12 5Q E Y D K S L S V 11 44 G S S V H Q K L V 11 55 P R E T Q E V F G 11 78F R N S E T S A S 11 13 V Q P E K R T G L 10 21 L R D E N G E C G 10 66V G D I V G R D L 10 68 D I V G R D L S I 10 85 A S E E E K Y D M 10 61V F G G G V G D I 9 72 R D L S I S F R N 9 24 E N G E C G Q T F 8 34 L KE E Q G R A F 8 53 N D P R E T Q E V 8 54 D P R E T Q E V F 8 58 T Q E VF G G G V 8 62 F G G G V G D I V 8 70 V G R D L S 1S F 8 9 K S L S V Q PE K 6 40 R A F R G S S V H 6 56 R E T Q E V F G G 6 64 G G V G D I V G R6 65 G V G D I V G R D 6 18 R T G L R D E N G 5 33 R L K E E Q G R A 522 R D E N G E C G Q 4 29 G Q T F R L K E E 4 49 Q K L V N D P R E 4 50K L V N D P R E T 4 67 G D I V G R D L S 4 79 R N S E T S A S E 4 2 G KC Q E Y D K S 3 7 Y D K S L S V Q P 3 19 T G L R D E N G E 3 20 G L R DE N G E C 3 60 E V F G G G V G D 3 63 G G G V G D I V G 3 76 I S F R N SE T S 3 11 L S V Q P E K R T 2 15 P E K R T G L R D 2 30 Q T F R L K E EQ 2 35 K E E Q G R A F R 2 36 E E Q G R A F R G 2 41 A F R G S S V H Q 245 S S V H Q K L V N 2 46 S V H Q K L V N D 2 52 V N D P R E T Q E 2 69I V G R D L S I S 2 74 L S I S F R N S E 2 81 S E T S A S E E E 2 1 M GK C Q E Y D K 1 4 C Q E Y D K S L S 1 8 D K S L S V Q P E 1 12 S V Q P EK R T G 1 23 D E N G E C G Q T 1 28 C G Q T F R L K E 1 31 T F R L K E EQ G 1 47 V H Q K L V N D P 1 59 Q E V F G G G V G 1 73 D L S I S F R N S1 80 N S E T S A S E E 1 83 T S A S E E E K Y 1 213P1F11 v.4: HLA-B*4402nonamers 26 G E C G Q T F R L 22 36 E E Q G R A F R G 15 3 K C Q E Y D KS L 13 24 E N G E C G Q T F 13 34 L K E E Q G R A F 13 5 Q E Y D K S L SV 12 13 V Q P E K R T G L 12 15 P E K R T G L R D 12 23 D E N G E C G QT 12 35 K E E Q G R A F R 12 43 R G S S V H Q K L 12 66 V G D I V G R DL 12 70 V G R D L S I S F 12 54 D P R E T Q E V F 11 56 R E T Q E V F GG 11 59 Q E V F G G G V G 11 68 D I V G R D L S I 11 81 S E T S A S E EE 11 83 T S A S E E E K Y 11 86 S E E E K Y D M S 11 61 V F G G G V G DI 10 12 S V Q P E K R T G 6 52 V N D P R E T Q E 6 60 E V F G G G V G D6 6 E Y D K S L S V Q 5 16 E K R T G L R D E 5 27 E C G Q T F R L K 5 37E Q G R A F R G S 5 41 A F R G S S V H Q 5 64 G G V G D I V G R 5 67 G DI V G R D L S 5 71 G R D L S I S F R 5 74 L S I S F R N S E 5 76 I S F RN S E T S 5 10 S L S V Q P E K R 4 28 C G Q T F R L K E 4 29 G Q T F R LK E E 4 40 R A F R G S S V H 4 44 G S S V H Q K L V 4 50 K L V N D P R ET 4 53 N D P R E T Q E V 4 84 S A S E E E K Y D 4 8 D K S L S V Q P E 314 Q P E K R T G L R 3 17 K R T G L R D E N 3 19 T G L R D E N G E 3 30Q T F R L K E E Q 3 42 F R G S S V H Q K 3 45 S S V H Q K L V N 3 46 S VH Q K L V N D 3 51 L V N D P R E T Q 3 57 E T Q E V F G G G 3 65 G V G DI V G R D 3 73 D L S I S F R N S 3 75 S I S F R N S E T 3 78 F R N S E TS A S 3 80 N S E T S A S E E 3 82 E T S A S E E E K 3 85 A S E E E K Y DM 3 7 Y D K S L S V Q P 2 9 K S L S V Q P E K 2 11 L S V Q P E K R T 218 R T G L R D E N G 2 21 L R D E N G E C G 2 31 T F R L K E E Q G 2 47V H Q K L V N D P 2 49 Q K L V N D P R E 2 55 P R E T Q E V F G 2 63 G GG V G D I V G 2 69 I V G R D L S I S 2 72 R D L S I S F R N 2 77 S F R NS E T S A 2 2 G K C Q E Y D K S 1 4 C Q E Y D K S L S 1 20 G L R D E N GE C 1 22 R D E N G E C G Q 1 25 N G E C G Q T F R 1 32 F R L K E E Q G R1 38 Q G R A F R G S S 1 39 G R A F R G S S V 1 48 H Q K L V N D P R 162 F G G G V G D I V 1 79 R N S E T S A S E 1 213P1F11 v.4: HLA-B*5101nonamers 54 D P R E T Q E V F 20 62 F G G G V G D I V 18 43 R G S S V HQ K L 16 66 V G D I V G R D L 16 68 D I V G R D L S I 16 5 Q E Y D K S LS V 15 40 R A F R G S S V H 14 61 V F G G G V G D I 14 84 S A S E E E KY D 13 13 V Q P E K R T G L 12 14 Q P E K R T G L R 11 3 K C Q E Y D K SL 10 19 T G L R D E N G E 10 28 C G Q T F R L K E 10 53 N D P R E T Q EV 10 63 G G G V G D I V G 10 44 G S S V H Q K L V 9 58 T Q E V F G G G V9 64 G G V G D I V G R 9 70 V G R D L S I S F 9 25 N G E C G Q T F R 826 G E C G Q T F R L 8 39 G R A F R G S S V 8 1 M G K C Q E Y D K 7 8 DK S L S V Q P E 7 38 Q G R A F R G S S 7 73 D L S I S F R N S 7 6 E Y DK S L S V Q 6 23 D E N G E C G Q T 5 34 L K E E Q G R A F 5 47 V H Q K LV N D P 5 51 L V N D P R E T Q 5 57 E T Q E V F G G G 5 76 I S F R N S ET S 5 9 K S L S V Q P E K 4 11 L S V Q P E K R T 4 21 L R D E N G E C G4 24 E N G E C G Q T F 4 32 F R L K E E Q G R 4 41 A F R G S S V H Q 442 F R G S S V H Q K 4 45 S S V H Q K L V N 4 65 G V G D I V G R D 4 80N S E T S A S E E 4 7 Y D K S L S V Q P 3 10 S L S V Q P E K R 3 12 S VQ P E K R T G 3 15 P E K R T G L R D 3 16 E K R T G L R D E 3 27 E C G QT F R L K 3 33 R L K E E Q G R A 3 36 E E Q G R A F R G 3 46 S V H Q K LV N D 3 48 H Q K L V N D P R 3 49 Q K L V N D P R E 3 59 Q E V F G G G VG 3 60 E V F G G G V G D 3 69 I V G R D L S I S 3 72 R D L S I S F R N 374 L S I S F R N S E 3 79 R N S E T S A S E 3 83 T S A S E E E K Y 3 86S E E E K Y D M S 3 2 G K C Q E Y D K S 2 20 G L R D E N G E C 2 29 G QT F R L K E E 2 31 T F R L K E E Q G 2 37 E Q G R A F R G S 2 50 K L V ND P R E T 2 52 V N D P R E T Q E 2 55 P R E T Q E V F G 2 56 R E T Q E VF G G 2 71 G R D L S I S F R 2 77 S F R N S E T S A 2 82 E T S A S E E EK 2 85 A S E E E K Y D M 2 17 K R T G L R D E N 1 30 Q T F R L K E E Q 175 S I S F R N S E T 1 78 F R N S E T S A S 1 213P1F11 v.4: RT1.A1nonamers 76 I S F R N S E T S 18 83 T S A S E E E K Y 18 60 E V F G G GV G D 17 85 A S E E E K Y D M 17 40 R A F R G S S V H 16 9 K S L S V Q PE K 14 30 Q T F R L K E E Q 13 24 E N G E C G Q T F 12 54 D P R E T Q EV F 12 12 S V Q P E K R T G 11 34 L K E E Q G R A F 11 5 Q E Y D K S L SV 10 70 V G R D L S I S F 10 51 L V N D P R E T Q 9 84 S A S E E E K Y D9 3 K C Q E Y D K S L 8 13 V Q P E K R T G L 8 32 F R L K E E Q G R 8 45S S V H Q K L V N 8 46 S V H Q K L V N D 8 74 L S I S F R N S E 8 11 L SV Q P E K R T 7 19 T G L R D E N G E 7 26 G E C G Q T F R L 7 66 V G D IV G R D L 7 69 I V G R D L S I S 7 80 N S E T S A S E E 7 43 R G S S V HQ K L 6 44 G S S V H Q K L V 6 49 Q K L V H D P R E 6 65 G V G D I V G RD 6 72 R D L S I S F R N 6 17 K R T G L R D E N 5 2 G K C Q E Y D K S 335 K E E Q G R A F R 3 50 K L V N D P R E T 3 81 S E T S A S E E E 3 86S E E E K Y D M S 3 4 C Q E Y D K S L S 2 10 S L S V Q P E K R 2 18 R TG L R D E N G 2 20 G L R D E N G E C 2 21 L R D E N G E C G 2 23 D E N GE C G Q T 2 28 C G Q T F R L K E 2 31 T F R L K E E Q G 2 33 R L K E E QG R A 2 38 Q G R A F R G S S 2 41 A F R G S S V H Q 2 47 V H Q K L V N DP 2 48 H Q K L V N D P R 2 53 N D P R E T Q E V 2 56 R E T Q E V F G G 261 V F G G G V G D I 2 62 F G G G V G D I V 2 64 G G V G D I V G R 2 67G D I V G R D L S 2 75 S I S F R N S E T 2 82 E T S A S E E E K 2 1 M GK C Q E Y D K 1 6 E Y D K S L S V Q 1 8 D K S L S V Q P E 1 14 Q P E K RT G L R 1 16 E K R T G L R D E TABLE XIXA, part 5: MHC Class 1 nonameranalysis of 213P1F11 v.5 (aa 1-242) 213P1F11 v.5: HLA-A *0201 nonamers 5A L I L R VT K A 24 2 A R L A L IL R V 20 3 R L A L I LR V T 20 6 L I LR V TK A R 14 7 I L R V T KA R E 14 4 L A L I L RV T K 13 1 G A R L A LIL R 9 8 L R V T K AR E G 5 9 R V T K A RE G S 4 213P1F11 v.5: HLA-A1nonamers 2 A R L A L I LR V 7 1 G A R L A L IL R 6 5 A L I L R V TK A 53 R L A L I L RV T 2 6 L I L R V T KA R 2 4 L A L I L R VT K 1 7 I L R VT K AR E 1 9 R V T K A R EG S 1 213P1F11 v.5: HLA-A26 nonamers 5 A L I LR V T K A 15 3 R L A L I L R V T 13 9 R V T K A R E G S 12 6 L I L R V TK A R 11 7 I L R V T K A R E 10 2 A R L A L I L R V 6 1 G A R L A L I LR 4 4 L A L I L R V T K 2 8 L R V T K A R E G 2 213P1F11 v.5: HLA-A3nonamers 4 L A LI L R VT K 22 3 R L AL I L RV T 20 5 A L IL R V TK A 206 L I LR V T KA R 19 7 I L RV T K AR E 18 9 R V TK A R EG S 15 2 A R LAL I LR V 10 1 C A RL A L IL R 8 8 L R VT K A RE G 4 213P1F11 v.5:HLA-B*0702 nonamers 2 A R L A L I L R V 11 5 A L I L R V T K A 10 3 R LA L I L R V T 9 7 I L R V T K A R E 4 4 L A L I L R V T K 3 9 R V T K AR E G S 3 1 G A R L A L I L R 2 6 L I L R V T K A R 2 213P1F11 v.5:HLA-B*08 nonamers 5 A L I L R V T K A 16 7 I L R V T K A R E 14 1 G A RL A L I L R 12 8 L R V T K A R E G 11 3 R L A L I L R V T 7 6 L I L R VT K A R 6 4 L A L I L R V T K 5 2 A R L A L I L R V 1 213P1F11 v.5:HLA-B*1510 nonamers 7 I L R V T K A R E 6 3 R L A L I L R V T 5 4 L A LI L R V T K 4 2 A R L A L I L R V 3 8 L R V T K A R E G 3 9 R V T K A RE G S 2 1 G A R L A L I L R 1 5 A L I L R V T K A 1 6 L I L R V T K A R1 213P1F11 v.5: HLA-B*2705 nonamers 2 A R L A L I L R V 20 1 G A R L A LI L R 16 4 L A L I L R V T K 15 8 L R V T K A R E G 14 6 L I L R V T K AR 13 5 A L I L R V T K A 9 3 R L A L I L R V T 8 9 R V T K A R E G S 6 7I L R V T K A R E 5 213P1F11 v.5: HLA-B*2709 nonamers 2 A R L A L I L RV 23 8 L R V T K A R E G 12 3 R L A L I L R V T 5 9 R V T K A R E G S 51 G A R L A L I L R 3 4 L A L I L R V T K 3 5 A L I L R V T K A 3 6 L TL R V T K A R 2 7 I L R V T K A R E 2 213P1F11 v.5: HLA-B*4402 nonamers5 A L l L R V T K A 10 2 A R L A L I L R V 8 6 L I L R V T K A R 7 2  RL A L I L R TABLE XIXA, part 6: MHC Class 1 nonamer analysis of 213P1F11v.6(aa 1-242) 213P1F11 v.6: HLA-A*0201 nonamers 1 K L E N L FE A M 16 8A M N N K NC Q A 16 4 N L F E A MN N K 14 9 M N N K N CQ A L 12 2 L E NL F EA M N 6 5 L F E A M NN K N 4 7 E A M N N KN C Q 3 6 F E A M N NK NC 2 3 E N L F E AM N N −2 213P1F11 v.6: HLA-A1 nonamers 1 K L E N L F EAM 14 5 L F E A M N NK N 13 6 F E A M N N KN C 2 8 A M N N K N CQ A 2 2 LE N L F E AM N 1 4 N L F E A M NN K 1 213P1F11 v.6: HLA-A26 nonamers 1 KL E N L F E A M 22 4 N L F E A M N N K 17 9 M N N K N C Q A L 11 3 E N LF E A M N N 8 5 L F E A M N N K N 7 7 E A M N N K N C Q 6 2 L E N L F EA M N 2 6 F E A M N N K N C 2 8 A M N N K N C Q A 2 213P1F11 v.6: HLA-A3nonamers 4 N L FE A M NN K 21 1 K L EN L F EA M 15 8 A M NN K N CQ A 8 3E N LF E A MN N 6 2 L E NL F E AM N 5 5 L F EA M N NK N 2 6 F E AM N NKN C 1 7 E A MN N K NC Q 1 9 M N NK N C QA L 1 213P1F11 v.6: HLA-B*0702nonamers 9 M N N K N C Q A L 12 1 K L E N L F E A M 9 8 A M N N K N C QA 8 7 E A M N N K N C Q 2 2 L E N L F E A M N 1 3 E N L F E A M N N 1 5L F E A M N N K N 1 6 F E A M N N K N C 1 213P1F11 v.6: HLA-B*08nonamers 8 A M N N K N C Q A 11 9 M N N K N C Q A L 11 4 N L F E A M N NK 8 1 K L E N L F E A M 7 7 E A M N N K N C Q 6 6 F E A M N N K N C 3 3E N L F E A M N N 2 2 L E N L F E A M N 1 5 L F E A M N N K N 1 213P1F11v.6: HLA-B*1510 nonamers 9 M N N K N C Q A L 13 1 K L E N L F E A M 8 7E A M N N K N C Q 3 4 N L F E A M N N K 2 6 F E A M N N K N C 2 3 E N LF E A M N N 1 5 L F E A M N N K N 1 213P1F1 v.6: HLA-B*2705 nonamers 4 NL F E A M N N K 17 9 M N N K N C Q A L 12 1 K L E N L F E A M 11 3 E N LF E A M N N 7 5 L F E A M N N K N 4 8 A M N N K N C Q A 4 6 F E A M N NK N C 3 2 L E N L F E A M N 2 7 E A M N N K N C Q 2 213P1F11 v.6:HLA-B*2709 nonamers 1 K L E N L F E A M 10 9 M N N K N C Q A L 10 3 E NL F E A M N N 4 4 N L F E A M N N K 3 8 A M N N K N C Q A 2 6 F E A M NN K N C 1 213P1F11 v.6: HLA-B*4402 nonamers 6 F E A M N N K N C 13 9 M NN K N C Q A L 13 2 L E N L F E A M N 11 7 E A M N N K N C Q 6 1 K L E NL F E A M 5 8 A M N N K N C Q A 5 3 E N L F E A M N N 4 4 N L F E A M NN K 4 5 L F E A M N N K N 2

[0770] TABLE XIXB MHC Class I Analysis of 213P1F11 (decamers). SEQ. Pos1 2 3 4 5 6 7 8 9 0 score ID NO. TABLE XIXB, part 1: MHC Class I decameranalysis of 213P1F11 v.1 (aa 1-242). 213P1F11 v.1: HLA-A*0201 decamers111 A L N N K N C Q A L 24 13 D M S G A R L A L I 23 86 L M A H G R E GF L 22 94 F L K G E D G E M V 22 119 A L R A K P K V Y I 22 142 T V G GD E I V M V 22 16 G A R L A L I L C V 20 226 K T N P E I Q S T L 20 157Q T I P T Y T D A L 19 185 S C F I Q T L V D V 19 200 G H I L E L L T EV 19 209 V T R R M A E A E L 19 19 L A L I L C V T K A 18 212 R M A E AE L V Q E 18 27 K A R E G S E E D L 17 37 D A L E H M F R Q L 17 56 P TA E Q F Q E E L 17 70 Q A I D S R E D P V 17 120 L R A K P K V Y I I 17162 Y T D A L H V Y S T 17 196 T K R K G H I L E L 17 205 L L T E V T RR M A 17 18 R L A L I L C V T K 16 103 V K L E N L F E A L 16 107 N L FE A L N N K N 16 150 M V I K D S P Q T I 16 165 A L H V Y S T V E G 16182 Q K G S C F I Q T L 16 197 K R K G H I L E L L 16 201 H I L E L L TE V T 16 12 Y D M S G A R L A L 15 96 K G E D G E M V K L 15 117 C Q A LR A K P K V 15 187 F I Q T L V D V F T 15 202 I L E L L T E V T R 15 20A L E L L V T K A R 14 21 L I L C V T K A R E 14 22 I L C V T K A R E G14 30 E G S E E D L D A L 14 75 R E D P V S C A F V 14 127 Y I I Q A C RG E Q 14 143 V G G D E I V M V I 14 149 V M V I K D S P Q T 14 163 T D AL H V Y S T V 14 170 S T V E G Y I A Y R 14 218 L V Q E G K A R K T 14222 G K A R K T N P E I 14 230 E I Q S T L R K R L 14 6 S L E E E K Y DM S 13 85 V L M A H G R E G F 13 102 M V K L E N L F E A 13 134 G E Q RD P G E T V 13 167 H V Y S T V E G Y I 13 175 Y I A Y R H D Q K G 13 204E L L T E V T R R M 13 233 S T L R K R L Y L Q 13 17 A R L A L I L C V T12 99 D G E M V K L E N L 12 104 K L E N L F E A L Q 13 193 D V F T KR K G H I 12 10 E K Y D M S G A R L 12 14 M S G A R L A L I L 11 38 A LE H M F R Q L R 11 41 H H F R Q L R F B S 11 45 Q L R F E S T M K R 1151 T H K R D P T A E Q 11 71 A I D S R E D P V S 11 77 D P V S C A F V VL 11 78 P V S C A F V V L M 11 159 I P T Y T D A L H V 11 183 K G S C FI Q T L V 11 194 V F T K R K G H I L 11 63 E E L E K F Q Q A I 10 79 V SC A F V V L M A 10 122 A K P K V Y I I Q A 10 128 I I Q A C R G E Q R 10140 G E T V G G D E I V 10 153 K D S P Q T I P T Y 10 158 T I P T Y T DA L H 10 190 T L V D V F T K R K 10 210 T R R M A E A E L V 10 232 Q S TL R K R L Y L 10 1 M S N P R S L E E E 9 5 R S L E E E K Y D M 9 35 D LD A L E H M F R 9 73 D S R E D P V S C A 9 84 V V L M A H G R E G 9 93 GF L K G E D G E M 9 151 V I K D S P Q T I P 9 213 M A E A E L V Q E G 9217 E L V Q E G K A R K 9 225 R K T N P E I Q S T 9 15 S G A R L A L I LC 8 5 S T M K R D P T A E 8 64 E L E K F Q Q A I D 8 80 S C A F V V L MA H 8 179 R H D Q K G S C F I 8 189 Q T L V D V F T K R 8 191 L V D V FT K R K G 8 199 K G H I L E L L T E 8 203 L E L L T E V T R R 8 207 T EV T R R M A E A 8 43 F R Q L R F E S T M 7 76 E D P V S C A F V V 7 81 CA F V V L M A H G 7 110 E A L N N K N C Q A 7 137 R D P G E T V G G D 7141 E T V G G D E I V M 7 147 E I V M V I K D S P 7 148 I V M V I K D SP Q 7 160 P T Y T D A L H V Y 7 176 I A Y R H D Q K G S 7 188 I Q T L VD V F T K 7 214 A E A E L V Q E G K 7 25 V T K A R E G S E E 6 42 M F RQ L R F E S T 6 72 I D S R E D P V S C 6 87 M A H G R E G F L K 6 89 H GR E G F L K G E 6 97 G E D G E M V K L E 6 101 E M V K L E N L F E 6 114N K N C Q A L R A K 6 125 K V Y I I Q A C R G 6 139 P G E T V G G D E I6 145 G D E I V M V I K D 6 152 T K D S P Q T I P T 6 166 L H V Y S T VE G Y 6 168 V Y S T V E G Y I A 6 171 T V E G Y I A Y R H 6 186 C F I QT L V D V F 6 206 L T E V T R R M A E 6 215 E A E L V Q E G K A 6 7 L EE E K Y D M S G 5 11 K Y D M S G A R L A 5 24 C V T K A R E G S E 5 29 RE G S E E D L D A 5 32 S E E D L D A L E H 5 33 E E D L D A L E H M 5 48F E S T M K R D P T 5 83 F V V L M A H G R E 5 88 A H G R E G F L K G 5112 L N N K N C Q A L R 5 115 K N C Q A L R A K P 5 118 Q A L R A K P KV Y 5 121 R A K P K V Y I I Q 5 123 K P K V Y I I Q A C 5 133 R G E Q RD P G E T 5 13 Q R D P G E T V G G 5 14 G G D E I V M V I K 5 155 S P QT I P T Y T D 5 164 D A L H V Y S T V E 5 198 R K G H I L E L L T 5 223K A R K T N P E I Q 5 229 P E I Q S T L R K R 5 2 S N P R S L E E E K 42 T K A R E G S E E D 4 31 G S E E D L D A L E 4 3 L D A L E H M F R Q 44 L R F E S T M K R D 4 58 A E Q F Q E E L E K 4 59 E Q F Q E E L E K F4 6 E K F Q Q A I D S R 4 82 A F V V L M A H G R 4 9 G R E G F L K G E D4 95 L K G E D G E M V K 4 105 L E N L F E A L N N 4 109 F E A L N N K NC Q 4 113 N N K N C Q A L R A 4 12 V Y I I Q A C R G E 4 129 I Q A C RG E Q R D 4 13 Q A C R G E Q R D P 4 131 A C R G E Q R D P G 4 132 C R GE Q R D P G E 4 14 D E I V M V I K D S 4 177 A Y R H D Q K G S C 4 181 DQ K G S C F I Q T 4 195 F T K R K G H I L E 4 21 A E L V Q E G K A R 423 L C V T K A R E G S 3 28 A R E G S E E D L D 3 3 L E H M F R Q L R F3 4 E S T M K R D P T A 3 53 K R D P T A E Q F Q 3 57 T A E Q F Q E E LE 3 62 Q E E L E K F Q Q A 3 68 F Q Q A I D S R E D 3 7 S R E D P V S CA F 3 10 G E M V K L E N L F 3 10 E N L F E A L N N K 3 15 D S P Q T I PT Y T 3 17 G Y I A Y R H D Q K 3 178 Y R H D Q K G S C F 3 219 V Q E G KA R K T N 3 3 N P R S L E E E K Y 2 4 R Q L R F E S T M K 2 61 F Q E E LE K F Q Q 2 69 Q Q A I D S R E D P 2 98 E D G E M V K L E N 2 161 T Y TD A L H V Y S 2 169 Y S T V E G Y I A Y 2 211 R R M A E A E L V Q 2 227T N P E I Q S T L R 2 231 I Q S T L R K R L Y 2 8 E E E K Y D M S G A 134 E D L D A L E H M F 2 40 E H M F R Q L R F E 1 52 M K R D P T A E Q F1 60 Q F Q E E L E K F Q 1 67 K F Q Q A I D S R E 1 138 D P G E T V G GD E 1 184 G S C F I Q T L V D 1 208 E V T R R M A E A E 1 224 A R K T NP E I Q S 1 47 R F E S T M K R D P −1 91 R E G F L K G E D G −1 92 E G FL K G E D G E −1 116 N C Q A L R A K P K −1 173 E G Y I A Y R H D Q −1124 P K V Y I I Q A C R −2 135 E Q R D P G E T V G −2 221 E G K A R K TN P E −3 4 P R S L E E E K Y D −4 9 E E K Y D M S G A R −4 213P1F11 v.1:HLA-A*0202 decamers 214 A E A E L V Q E G K 4 15 S G A R L A L I L C 318 R L A L I L C V T K 3 26 T K A R E G S E E D 3 36 L D A L E H M F R Q3 56 P T A E Q F Q E E L 3 69 Q Q A I D S R E D P 3 80 S C A F V V L M AH 3 86 L M A H G R E G F L 3 109 F E A L N N K N C Q 3 117 C Q A L R A KP K V 3 120 L R A K P K V Y I I 3 129 I Q A C R G E Q R D 3 163 T D A LH V Y S T V 3 175 Y I A Y R H D Q K G 3 212 R M A E A E L V Q E 3 222 GK A R K T N P E I 3 16 G A R L A L I L C V 2 19 L A L I L C V T K A 2 27K A R E G S E E D L 2 37 D A L E H M F R Q L 2 57 T A E Q F Q E E L E 270 Q A I D S R E D P V 2 81 C A F V V L M A H G 2 87 M A H G R E G F L K2 110 E A L N N K N C Q A 2 118 Q A L R A K P K V Y 2 121 R A K P K V YI I Q 2 130 Q A C R G E Q R D P 2 164 D A L H V Y S T V E 2 176 I A Y RH D Q K G S 2 213 E A E L V Q E G K A 2 223 K A R K T N P E I Q 2 17 A AL A L I L C V T 1 20 A L I L C V T K A R 1 28 A R E G S E E D L D 1 38 AL E H M F R Q L R 1 58 A E Q F Q E E L E K 1 71 A I D S R E D P V S 1 82A F V V L M A H G R 1 88 A H G R E G F L K G 1 111 A L N N K N C Q A L 1119 A L R A K P K V Y I 1 122 A K P K V Y I I Q A 1 131 A C R G E Q R DP G 1 165 A L H V Y S T V E G 1 177 A Y R H D Q K G S C 1 216 A E L V QE G K A R 1 224 A R K T N P E I Q S 1 213P1F11 v.1: HLA-A *0203 decamers207 T E V T R R M A E A 18 8 E E E K Y D M S G A 10 11 K Y D M S G A R LA 10 19 L A L I L C V T K A 10 29 R E G S E E D L D A 10 49 E S T M K RD P T A 10 62 Q E E L E K F Q Q A 10 73 D S R E D P V S C A 10 79 V S CA F V V L M A 10 102 M V K L E N L F E A 10 110 E A L N N K N C Q A 10113 N N K N C Q A L R A 10 122 A K P K V Y I I Q A 10 156 P Q T I P TY T D A 10 168 V Y S T V E G Y I A 10 205 L L T E V T R R M A 10 215 EA E L V Q E G K A 10 9 E E K Y D M S G A R 9 12 Y D N S G A R L A L 9 20A L I L C V T K A R 9 30 E G S E E D L D A L 9 50 S T M K R D P T A E 963 E E L E K F Q Q A I 9 74 S R E D P V S C A F 9 80 S C A F V V L M A H9 103 V K L E N L F E A L 9 111 A L N N K N C Q A L 9 114 N K N C Q AL R A K 9 123 K P K V Y I I Q A C 9 157 Q T I P T Y T D A L 9 169 Y S TV E G Y I A Y 9 206 L T E V T R R M A E 9 208 E V T R R M A E A E 9 216A E L V Q E G K A R 9 10 E K Y D M S G A R L 8 13 D M S G A R L A L I 821 L I L C V T K A R E 8 31 G S E E D L D A L E 8 51 T M K R D P T A E Q8 64 E L E K F Q Q A I D 8 75 R E D P V S C A F V 8 81 C A F V V L M A HG 8 104 K L E N L F E A L N 8 112 L N N K N C Q A L R 8 115 K N C Q A LR A K P 8 124 P K V Y I I Q A C R 8 158 T I P T Y T D A L H 8 170 S T VE G Y I A Y R 8 209 V T R R M A E A E L 8 217 E L V Q E G K A R K 8213P1F11 v.1: HLA-A1 decamers 169 Y S T V E G Y I A Y 25 160 P T Y T D AL H V Y 22 153 K D S P Q T I P T Y 19 162 Y T D A L H V Y S T 19 32 SE E D L D A L E H 18 3 N P R S L E E E K Y 17 145 G D E I V M V I K D 17206 L T E V T R R M A E 17 231 I Q S T L R K R L Y 17 31 G S E E D L D AL E 16 118 Q A L R A K P K V Y 16 166 L H V Y S T V E G Y 16 228 N P E IQ S T L R K 16 38 A L E H M F R Q L R 15 6 S L E E E K Y D M S 14 28 AR E G S E E D L D 14 53 K R D P T A E Q F Q 14 75 R E D P V S C A F V 1497 G E D G E M V K L E 14 136 Q R D P G E T V G G 14 152 I K D S P Q T IP T 14 62 Q E E L E K F Q Q A 13 79 V S C A F V V L M A 13 104 K L E N LF E A L N 13 195 F T K R K G H I L E 13 219 V Q E G K A R K T N 13 11 KY D M S G A R L A 12 57 T A E Q F Q E E L E 12 71 A I D S R E D P V S 1274 S R E D P V S C A F 12 88 A H G R E G F L K G 12 96 K G E D G E M V KL 12 141 E T V G G D E I V M 12 191 L V D V F T K R K G 12 215 E A E L VQ E G K A 12 35 D L D A L E H M F R 11 61 F Q E E L E K F Q Q 11 64 EL E K F Q Q A I D 11 90 G R E G F L K G E D 11 108 L F E A L N N K N C11 139 P G E T V G G D E I 11 171 T V E G Y I A Y R H 11 184 G S C F I QT L V D 11 189 Q T L V D V F T K R 11 202 I L E L L T E V T R 11 213 MA E A E L V Q E G 11 232 Q S T L R K R L Y L 11 7 L E E E K Y D M S G 108 E E E K Y D M S G A 10 14 M S G A R L A L I L 10 33 E E D L D A L E HM 10 47 R F E S T M K R D P 10 99 D G E M V K L E N L 10 133 R G E Q R DP C E T 10 144 G G D E I V M V I K 10 157 Q T I P T Y T D A L 10 179 RH D Q K G S C F I 10 226 K T N P E I Q S T L 10 233 S T L R K R L Y L Q10 12 Y D M S G A R L A L 9 1 M S N P R S L E E E 8 15 S G A R L A L I LC 8 25 V T K A R E G S E E 8 50 S T N K R D P T A E 8 121 R A K P K VY I I Q 8 170 S T V E G Y I A Y R 8 181 D Q K G S C F I Q T 8 198 R K GH I L E L L T 8 58 A E Q F Q E E L E K 7 101 E M V K L E N L F E 7 209 VT R R M A E A E L 7 211 R R M A E A E L V Q 7 16 G A R L A L I L C V 629 R E G S E E D L D A 6 39 L E H M F R Q L R F 6 56 P T A E Q F Q E E L6 98 E D G E M V K L E N 6 105 L E N L F E A L N N 6 113 N N K N C Q A LR A 6 159 I P T Y T D A L H V 6 196 T K R K G H I L E L 6 199 K G H I LE L L T E 6 73 D S R E D P V S C A 5 94 F L K G E D G E M V 5 122 A K PK V Y I I Q A 5 224 A R K T N P E I Q S 10 5 R S L E E E K Y D M 4 49 ES T M K R D P T A 4 65 L E K F Q Q A I D S 4 77 D P V S C A F V V L 4 87M A H G R E G F L K 4 103 V K L E N L F E A L 4 107 N L F E A L N N K N4 154 D S P Q T I P T Y T 4 175 Y T A Y R H D Q K G 4 13 D M S G A R L AL I 3 19 L A L I L C V T K A 3 37 D A L E H M F R Q L 3 42 M F R Q L RF E S T 3 45 Q L R F E S T M K R 3 55 D P T A E Q F Q E E 3 78 P V S C AF V V L M 3 85 V L N A H G R E G F 3 115 K N C Q A L R A K P 3 127 Y T IQ A C R G E Q 3 131 A C R G E Q R D P G 3 143 V G G D E I V M V I 3 178Y R H D Q K G S C F 3 197 K R K G H I L E L L 3 205 L L T E V T R R M A3 2 S N P R S L E E E K 2 17 A R L A L I L C V T 2 20 A L I L C V T K AR 2 48 F E S T M K R D P T 2 59 E Q F Q E E L E K F 2 80 S C A F V V L MA H 2 84 V V L M A H G R E G 2 100 G E M V K L E N L F 2 111 A L N N K NC Q A L 2 112 L N N K N C Q A L R 2 117 C Q A L R A K P K V 2 119 A L RA K P K V Y I 2 137 R D P G E T V G G D 2 142 T V G G D E I V M V 2 155S P Q T I P T Y T D 2 158 T T P T Y T D A L H 2 165 A L H V Y S T V E G2 168 V Y S T V E G Y I A 2 183 K G S C F I Q T L V 2 185 S C F I Q TL V D V 2 186 C F I Q T L V D V F 2 192 V D V F T K R K G H 2 194 V F TK R K G H I L 2 210 T R R M A E A E L V 2 216 A E L V Q E G K A R 2 218L V Q E G K A R K T 2 227 T N P E I Q S T L R 2 229 P E I Q S T L R K R2 10 E K Y D M S G A R L 1 18 R L A L I L C V T K 1 22 I L C V T K A R EG 1 23 L C V T K A R E G S 1 34 E D L D A L E H M F 1 41 H M F R Q L R FE S 1 43 F R Q L R F E S T M 1 44 R Q I I R F E S T M 1 68 F Q Q A I DS R E D 1 69 Q Q A I D S R E D P 1 76 E D P V S C A F V V 1 82 A F V V LM A H G R 1 83 F V V L M A H G R E 1 91 R E G F L K G E D G 1 95 L K G ED G E M V K 1 109 F E A L N N K N C Q 1 110 E A L N N K N C Q A 1 120 LR A K P K V Y I I 1 126 V Y I I Q A C R G E 1 128 I I Q A C R G H Q R 1134 G E Q R D P G E T V 1 135 E Q R D P G E T V G 1 138 D P G E T V G GD E 1 149 V M V I K D S P Q T 1 151 V I K D S P Q T I P 1 164 D A L H VY S T V E 1 172 V E G Y I A Y R H D 1 173 E G Y I A Y R H D Q 1 177 AY R H D Q K G S C 1 187 F I Q T L V D V F T 1 188 I L Q T L V D V F T K190 T L V D V F T K R K 1 201 H I L E L L T E V T 1 203 L E L L T E V TR R 1 204 E L L T E V T R R M 1 214 A E A E L V Q E G K 1 217 E L V Q EG K A R K 1 222 G K A R K T N P E I 1 230 E I Q S T L R K R L 12131P1511 v.1: HLA-A26 decamers 141 E T V G G D E I V M 26 230 E T Q S TL R K R L 26 59 E Q F Q E E L E K F 24 160 P T Y T D A L H V Y 24 78 P VS C A F V V L M 23 157 Q T I P T Y T D A L 23 186 C F I Q T L V D V F 23204 E L L T E V T R R M 23 56 P T A E Q F Q E E L 22 30 E G S E E D L DA L 21 37 D A L E H M F R Q L 21 226 K T N P E I Q S T L 21 33 E E D L DA L E H M 20 77 D P V S C A F V V L 20 209 V T R R M A E A E L 20 85 V LM A H G R E G F 19 99 D G E M V K L E N L 19 193 D V F T K R K G H I 1934 E D L D A L E H M F 18 111 A L N N K N C Q A L 18 142 T V G G D E I VM V 18 10 E K Y D M S G A R L 17 147 E I V M V I K D S P 17 153 K D S PQ T I P T Y 17 170 S T V E G Y I A Y R 17 208 E V T R R M A E A E 17 217E L V Q E 0 K A R K 17 35 D L D A L E H M F R 6 64 E L E K F Q Q A I D16 93 G F L K G E D G E M 16 102 M V K L E N L F E A 16 162 Y T D A L HV Y S T 16 6 S L E E E K Y D M S 15 96 K G E D G E M V K L 15 103 V K LE N L F E A L 15 166 L H V Y S T V E G Y 15 169 Y S T V E G Y I A Y 15189 Q T L V D V F T K R 15 194 V F T K R K G H I L 15 197 K R K G H I LE L L 15 66 E K F Q Q A I D S R 14 127 Y I I Q A C R G E Q 14 150 M V IK D S P Q T I 14 181 D Q K G S C F I Q T 14 182 Q K G S C F I Q T L 14196 T K R K G H I L E L 14 233 S T L R K R L Y L Q 14 8 E E E K Y D M SG A 13 13 D M S G A R L A L I 13 25 V T K A R E G S E E 13 71 A I D S RE D P V S 13 73 D S R E D P V S C A 13 107 N L F E A L N N K N 13 171 TV E G Y I A Y R H 13 175 Y I A Y R H D Q K G 13 218 L V Q E G K A R K T13 3 N P R S L E E E K Y 12 21 L I L C V T K A R E 12 24 C V T K A R E GS E 12 42 M F R Q L R F E S T 12 50 S T M K R D P T A E 12 52 M K R D PT A E Q F 12 55 D P T A E Q F Q E E 12 74 S R E D P V S C A F 12 94 F LK G E D G E M V 12 146 D E I V M V I K D S 12 151 V I K D S P Q T I P 12158 T I P T Y T D A L H 12 178 Y R H D Q K G S C F 12 191 L V D V F T KR K G 12 201 H I L E L L T E V T 12 206 L T E V T R R M A E 12 20 A L IL C V T K A R 11 39 L E H M F R Q L R F 11 83 F V V L M A H G R E 11 84V V L M A H G R E G 11 106 E N L F E A L N N K 11 125 K V Y I I Q A C RG 11 128 I I Q A C R G E Q R 11 148 I V M V I K D S P Q 11 167 H V Y S TV E G Y I 11 187 F I Q T L V D V F T 11 195 F T K R K G H I L E 11 205 LL T E V T R R M A 11 5 R S L E E E K Y D M 10 12 Y D M S G A R L A L 1018 R L A L I L C V T K 10 27 K A R E G S E E D L 10 40 E H M F R Q L R FE 10 45 Q L R F E S T M K R 10 63 E E L E K F Q Q A I 10 100 G E M V K LE N L F 10 118 Q A L R A K P K V Y 10 165 A L H V Y S T V E G 10 190 T LV D V F T K R K 10 231 I Q S T L R K R L Y 10 22 I L C V T K A R E G 938 A L E H M F R Q L R 9 43 F R Q L R F E S T M 9 46 L R F E S T M K R D9 67 K F Q Q A I D S R E 9 86 L M A H G R E G F L 9 92 E G F L K G E D GE 9 98 E D G E M V K L E N 9 104 K L E N L F E A L N 9 119 A L R A K P KV Y I 9 202 I L E L L T E V T R 9 212 R M A E A E L V Q E 9 9 E E K Y DM S G A R 8 14 M S G A R L A L I L 8 60 Q F Q E E L E K F Q 8 81 C A F VV L M A H G 8 137 R D P G E T V G G D 8 138 D P G E T V G G D E 8 144 GG D E I V M V I K 8 154 D S P Q T I P T Y T 8 229 P E I Q S T L R K R 8232 Q S T L R K R L Y L 8 1 M S N P R S L E E E 7 47 R F E S T M K R D P7 49 E S T M K R D P T A 7 76 E D P V S C A F V V 7 80 S C A F V V L M AH 7 82 A F V V L M A H G R 7 89 H G R E G F L K G E 7 97 G E D G E M V KL E 7 101 E M V K L E N L F E 7 108 L F E A L N N K N C 7 110 E A L N NK N C Q A 7 121 R A K P K V Y I I Q 7 122 A K P K V Y I I Q A 7 123 K PK V Y I I Q A C 7 135 E Q R D P G E T V G 7 185 S C F I Q T L V D V 7200 G H I L E L L T E V 7 215 E A E L V Q E G K A 7 221 E G K A R K T NP E 7 36 L D A L E H M F R Q 6 62 Q E E L E K F Q Q A 6 120 L R A K P KV Y I I 6 143 V G G D E I V M V I 6 163 T D A L H V Y S T V 6 164 D A LH V Y S T V E 6 173 E G Y I A Y R H D Q 6 207 T E V T R R M A E A 6 213M A E A E L V Q E G 6 225 R K T N P E I Q S T 6 15 S G A R L A L I L C 519 L A L T L C V T K A 5 79 V S C A F V V L M A 5 88 A H G R E G F L K G5 114 N K N C Q A L R A K 5 136 Q R D P G E T V G G 5 145 G D E I V M VI K D 5 172 V E G Y I A Y R H D 5 203 L E L L T E V T R R 5 7 L E E E KY D M S G 4 16 G A R L A L I L C V 4 17 A R L A L I L C V T 4 53 K R D PT A E Q F Q 4 75 R E D P V S C A F V 4 132 C R G E Q R D P G E 4 156 P QT I P T Y T D A 4 188 I Q T L V D V F T K 4 199 K G H I L E L L T E 4214 A E A E L V Q E G K 4 31 G S E E D L D A L E 3 41 H M F R Q L R F ES 3 51 T M K R D P T A E Q 3 61 F Q E E L E K F Q Q 3 70 Q A I D S R E DP V 3 90 G R E G F L K G E D 3 95 L K G E D G E M V K 3 115 K N C Q A LR A K P 3 117 C Q A L R A K P K V 3 126 V Y I I Q A C R G E 3 129 I Q AC R G E Q R D 3 174 G Y I A Y R H D Q K 3 222 G K A R K T N P E I 3 227T N P E I Q S T L R 3 2 S N P R S L E E E K 2 26 T K A R E G S E E D 228 A R E G S E E D L D 2 32 S E E D L D A L E H 2 54 R D P T A E Q F Q E2 72 I D S R E D P V S C 2 87 M A H G R E G F L K 2 112 L N N K N C Q AL R 2 113 N N K N C Q A L R A 2 131 A C R G E Q R D P G 2 133 R G E Q RD P G E T 2 149 V M V I K D S P Q T 2 152 I K D S P Q T I P T 2 161 T YT D A L H V Y S 2 179 R H D Q K G S C F I 2 219 V Q E G K A R K T N 2220 Q E G K A R K T N P 2 224 A R K T N P E I Q S 2 11 K Y D M S C A R LA 2 23 L C V T K A R E G S 1 29 R E G S E E D L D A 1 44 R Q L R F E S TM K 1 57 T A E Q F Q E E L E 1 58 A E Q F Q E E L E K 1 65 L E K F Q Q AI D S 1 68 F Q Q A I D S R E D 1 69 Q Q A I D S R E D P 1 105 L E N L FE A L N N 1 109 F E A L N N K N C Q 1 124 P K V Y I I Q A C R 1 13 P G ET V G G D E I 1 159 T P T Y T D A L H V 1 17 I A Y R H D Q K G S 1 177 AY R H D Q K G S C 1 180 H D Q K G S C F I Q 1 192 V D V F T K R K G H 1216 A E L V Q E G K A R 1 223 K A R K T N P E I Q 1 228 N P E I Q S T LR K 1 213P1F11 v.1: HLA-A3 decamers 18 R L A L I L C V T K 34 202 I LE L L T E V T R 25 217 E L V Q E G K A R K 23 20 A L I L C V T K A R 22119 A L R A K P K V Y I 22 128 I I Q A C R G E Q R 22 44 R Q L R F E S TM K 21 125 K V Y T I Q A C R G 21 190 T L V D V F T K R K 21 45 Q L R FE S T M K R 20 171 T V E G Y I A Y R H 19 38 A L E H M F R Q L R 18 118Q A L R A K P K V Y 18 150 M V I K D S P Q T I 18 174 G Y I A Y R H D QK 18 35 D L D A L E H M F R 17 85 V L M A H G R E G F 17 94 F L K G ED G E M V 17 104 K L E N L F E A L N 17 142 T V G G D E I V M V 17 165 AL H V Y S T V E G 17 188 I Q T L V D V F T K 17 208 E V T R R M A E A E17 58 A E Q F Q E E L E K 16 95 L K G E D G E M V K 16 153 K D S P QT I P T Y 16 22 I L C V T K A R E G 15 71 A I D S R E D P V S 15 84 V VL M A H G R E G 15 87 M A H G R E G F L K 15 111 A L N N K N C Q A L 15116 N C Q A L R A K P K 15 144 G G D E I V M V I K 15 148 I V M V IK D S P Q 15 158 T I P T Y T D A L H 15 167 H V Y S T V E G Y I 15 201 HI L E L L T E V T 15 214 A E A E L V Q E G K 15 2 S N P R S L E E E K 1452 M K R D P T A E Q F 14 78 P V S C A F V V L M 14 160 P T Y T D A L HV Y 14 218 L V Q E G K A R K T 14 228 N P E I Q S T L R K 14 6 S L E E EK Y D M S 13 21 L I L C V T K A R E 13 24 C V T K A R E G S E 13 64 E LE K F Q Q A I D 13 127 Y I I Q A C R G E Q 13 205 L L T E V T R R M A 13211 R R M A E A E L V Q 13 212 R M A E A E L V Q E 13 216 A E L V QE G K A R 13 226 K T N P E I Q S T L 13 32 S E E D L D A L E H 12 72 I DS R E D P V S C 12 83 F V V L M A H G R E 12 102 M V K L E N L F E A 12106 E N L F E A L N N K 12 187 F I Q T L V D V F T 12 204 E L L T EV T R R M 12 10 E K Y D M S G A R L 11 17 A R L A L I L C V T 11 107 N LF E A L N N K N 11 114 N K N C Q A L R A K 11 151 V I K D S P Q T I P 11178 Y R H D Q K G S C F 11 186 C F I Q T L V D V F 11 193 D V F T KR K G H I 11 199 K G H I L E L L T E 11 75 R E D P V S C A F V 10 82 A FV V L M A H G R 10 134 G E Q R D P G E T V 10 147 E I V M V I K D S P 11191 L V D V F T K R K G 10 3 N P R S L E E E K Y 9 25 V T K A R E G S EE 9 88 A H G R E G F L K G 9 131 A C R G E Q R D P G 9 135 E Q R D PG E T V G 9 136 Q R D P G E T V G G 9 157 Q T I P T Y T D A L 9 163 T DA L H V Y S T V 9 170 S T V E G Y I A Y R 9 175 Y I A Y R H D Q K G 9176 I A Y R H D Q K G S 9 177 A Y R H D Q K G S C 9 189 Q T L V D V F TK R 9 209 V T R R M A E A E L 9 230 E I Q S T L R K R L 9 14 M S G A RL A L I L 8 34 E D L D A L E H H F 8 43 F R Q L R F E S T M 8 77 D P V SC A F V V L 8 80 S C A F V V L M A H 8 96 K G E D G E M V K L 8 113 N NK N C Q A L R A 8 121 R A K P K V Y I I Q 8 159 I P T Y T D A L H V 8203 L E L L T E V T R R 8 231 I Q S T L R K R L Y 8 5 R S L E E E K Y DM 7 9 E E K Y D M S G A R 7 16 G A R L A L I L C V 7 27 K A R E G S E ED L 7 29 R E G S E E D L D A 7 39 L E H M F R Q L R F 7 51 T M K R DP T A E Q 7 54 R D P T A E Q F Q E 7 73 D S R E D P V S C A 7 74 S R E DP V S C A F 7 76 E D P V S C A F V V 7 91 R E G F L K G E D G 7 105 L EN L F E A L N N 7 112 L N N K N C Q A L R 7 115 K N C Q A L R A K P 7124 P K V Y I I Q A C R 7 137 R D P G E T V G G D 7 165 D A L H V Y S TV E 7 169 Y S T V E G Y T A Y 7 184 G S C F I Q T L V D 7 198 R K G H IL E L L T 7 219 V Q E G K A R K T N 7 223 K A R K T N P E I Q 7 224 A RK T N P E I Q S 7 225 R K T N P E I Q S T 7 229 P E I Q S T L R K R 7232 Q S T L R K R L Y L 7 11 K Y D M S G A R L A 6 37 D A L E H M F R QL 6 53 K R D P T A E Q F Q 6 62 Q E E L E K F Q Q A 6 66 E K F Q Q A I DS R 6 67 K F Q Q A I D S R E 6 70 Q A I D S R E D P V 6 79 V S C A FV V L M A 6 110 E A L N N K N C Q A 6 122 A K P K V Y T I Q A 6 133 R GE Q R D P G E T 6 141 E T V G G D E I V M 6 143 V G G D E I V M V I 6166 L H V Y S T V E G Y 6 173 E G Y I A Y R H D Q 6 181 D Q K G S C F IQ T 6 182 Q K G S C F I Q T L 6 185 S C F I Q T L V D V 6 196 T K R K GH I L E I 6 197 K R K G H I L E L L 6 210 T R R M A E A E L V 6 227 T NP E I Q S T L R 6 233 S T L R K R L Y L Q 6 12 Y D M S G A R L A L 5 13D M S G A R L A L I 5 15 S G A R L A L I L C 5 28 A R E G S E E D L D 542 M F R Q L R F E S T 5 69 Q Q A I D S R E D P 5 123 K P K V Y I I Q AC 5 130 Q A C R G E Q R D P 5 138 D P G E T V G G D E S 155 S P Q T IP T Y T D 5 161 T Y T D A L H V Y S 5 192 V D V F T K R K G H 5 200 G HI L E L L T E V 5 7 L E E E K Y D M S G 4 19 L A L I L C V T K A 4 26 TK A R E G S E E D 4 31 G S E E D L D A L E 4 41 H M F R Q L R F E S 4 47R F E S T M K R D P 4 49 E S T M K R D P T A 4 50 S T M K R D P T A E 459 E Q F Q E E L E K F 4 61 F Q E E L E K F Q Q 4 63 E E L E K F Q Q A I4 65 L E K F Q Q A I D S 4 89 H G R E G F L K G E 4 98 E D G E M V K L EN 4 100 G E M V K L E N L F 4 103 V K L E N L F E A L 4 126 V Y I I QA C R G E 4 149 V M V I K D S P Q T 3 162 Y T D A L H V Y S T 4 179 R HD Q K G S C F I 4 183 K G S C F I Q T L V 4 195 F T K R K G H I L E 4222 G K A R K T N P E I 4 1 M S N P R S L E E E 3 8 E E E K Y D M S G A3 60 Q F Q E E L E K F Q 3 81 C A F V V L M A H G 3 90 G R E G F L K G ED 3 93 G F L K G E D G E M 3 101 E M V K L E N L F E 3 129 I Q A C RG E Q R D 3 139 P G E T V G G D E I 3 146 D E I V M V I K D S 3 168 V YS T V E G Y I A 3 194 V F T K R K G H I L 3 206 L T E V T R R M A E 3207 T E V T R R M A E A 3 220 Q E G K A R K T N P 3 221 E G K A R K T NP E 3 30 E G S E E D L D A L 2 36 L D A L E H M F R Q 2 55 D P T A EQ F Q E E 2 56 P T A E Q F Q E E L 2 68 F Q Q A I D S R E D 2 86 L M A HG R E G F L 2 97 G E D G E M V K L E 2 108 L F E A L N N K N C 2 109 F EA L N N K N C Q 2 117 C Q A L R A K P K V 2 152 I K D S P Q T I P T 2154 D S P Q T I P T Y T 2 156 P Q T I P T Y T D A 2 213 M A E A E L V QE G 2 215 E A E L V Q E G K A 2 4 P R S L E E E K Y D 1 23 L C V T KA R E G S 1 33 E E D L D A L E H M 1 46 L R F E S T M K R D 1 48 F E S TM K R D P T 1 92 E G F L K G E D G E 1 12 L R A K P K V Y I I 1 132 C RG E Q R D P G E 1 145 G D E T V M V I K D 1 213P1F11 v.1: HLA-B*0702decamers 77 D P V S C A F V V L 24 +TL,32 159 I P T Y T D A L H V 19 12Y D M S G A R L A L 15 196 T K R K C H I L E L 15 14 M S G A R L A L I L14 3 E G S E E D L D A L 14 27 K A R E G S E E D L 13 9 K G E D G E M VK L 13 111 A L N N K N C Q A L 13 119 A L R A K P K V Y I 13 157 Q T I PT Y T D A L 13 197 K R K G H I L E L L 13 209 V T R R M A E A E L 13 228N P E I Q S T L R K 13 232 Q S T L R K R L Y L 13 3 N P R S L E E E K Y12 10 E K Y D M S G A R L 12 55 D P T A E Q F Q E E 12 86 L M A H G R EG F L 12 103 V K L E N L F E A L 12 123 K P K V Y I I Q A C 12 226 K T NP E I Q S T L 12 230 E I Q S T L R K R L 12 13 D M S G A R L A L I 11 37D A L E H M F R Q L 11 56 P T A E Q F Q E E L 11 75 R E D P V S C A F V11 78 P V S C A F V V L M 11 138 D P G E T V G G D E 11 142 T V G G D EI V M V 11 155 S P Q T I P T Y T D 11 182 Q K G S C F I Q T L 11 194 V FT K R K G H I L 11 16 G A R L A L I L C V 10 17 A R L A L I L C V T 1029 R E G S E E D L D A 10 48 F E S T M K R D P T 10 79 V S C A F V V L MA 10 99 D G E M V K L E N L 10 141 E T V G G D E I V M 10 152 I K D S PQ T I P T 10 183 K G S C F I Q T L V 10 198 R K G H I L E L L T 10 42 MF R Q L R F E S T 9 73 D S R E D P V S C A 9 85 V L M A H G R E G F 9120 L R A K P K V Y I I 9 122 A K P K V Y I I Q A 9 143 V G G D E I V MV I 9 162 Y T D A L H V Y S T 9 179 R H D Q K G S C F I 9 181 D Q K G SC F I Q T 9 187 F I Q T L V D V F T 9 8 E E E K Y D M S G A 8 11 K Y D MS G A R L A 8 19 L A L I L C V T K A 8 33 E E D L D A L E H M 8 39 L E HM F R Q L R F 8 49 E S T M K R D P T A 8 52 M K R D P T A E Q F 8 63 E EL E K F Q Q A I 8 76 E D P V S C A F V V 8 94 F L K G E D G E M V 8 113N N K N C Q A L R A 8 117 C Q A L R A K P K V 8 131 A C R G E Q R D P G8 168 V Y S T V E G Y I A 8 185 S C F I Q T L V D V 8 186 C F I Q T L VD V F 8 201 H I L E L L T E V T 8 204 E L L T E V T R R M 8 210 T R R MA E A E L V 8 222 G K A R K T N P E I 8 5 R S L E E E K Y D M 7 34 E D LD A L E H M F 7 59 E Q F Q E E L E K F 7 62 Q E E L E K F Q Q A 7 70 Q AI D S R E D P V 7 74 S R E D P V S C A F 7 93 G F L K G E D G E M 7 100G E M V K L E N L F 7 110 E A L N N K N C Q A 7 133 R G E Q R D P G E T7 149 V M V I K D S P Q T 7 150 M V I K D S P Q T I 7 154 D S P Q T I PT Y T 7 156 P Q T I P T Y T D A 7 163 T D A L H V Y S T V 7 200 G H I LE L L T E V 7 205 L L T E V T R R H A 7 207 T E V T R R M A E A 7 215 EA E L V Q E G K A 7 225 R K T N P E I Q S T 7 43 F R Q L R F E S T M 688 A H G R E G F L K G 6 102 M V K L E N L F E A 6 134 G E Q R D P G E TV 6 139 P G E T V G G D E I 6 140 G E T V G G D E I V 6 167 H V Y S T VE G Y I 6 178 Y R H D Q K G S C F 6 193 D V F T K R K G H I 6 211 R R MA E A E L V Q 6 218 L V Q E G K A R K T 6 71 A I D S R E D P V S 5 72 ID S R E D P V S C 5 101 E H V K L E N L F E 5 135 E Q R D P G E T V G 5136 Q R D P G E T V G G 5 153 K D S P Q T I P T Y 5 165 A L H V Y S T VE G 5 18 R L A L I L C V T K 4 20 A L I L C V T K A R 4 28 A R E G S E ED L D 4 50 S T M K R D P T A E 4 53 K R D P T A E Q F Q 4 58 A E Q F Q EE L E K 4 97 G E D G E M V K L E 4 98 E P G E M V K L E N 4 137 R P P GE T V G G D 4 177 A Y R H D Q K G S C 4 184 G S C F I Q T L V D 4 212 RM A E A E L V Q E 4 221 E G K A R K T N P E 4 223 K A R K T N P E I Q 435 D L D A L E H M F R 3 38 A L E H M F R Q L R 3 40 E H M F R Q L R F E3 45 Q L R F E S T M K R 3 64 E L E K F Q Q A I D 3 115 K N C Q A L R AK P 3 144 G G D E I V M V I K 3 148 T V M V I K D S P Q 3 199 K G H I LE L L T E 3 202 I L E L L T E V T R 3 214 A E A E L V Q E G K 3 216 A EL V Q E G K A R 3 219 V Q E G K A R K T N 3 220 Q E G K A R K T N P 3231 I Q S T L R K R L Y 3 4 P R S L E E E K Y D 2 9 E E K Y D M S G A R2 32 S E E D L D A L E H 2 44 R Q L R F E S T H K 2 51 T H K R D P T A EQ 2 69 Q Q A I D S R E D P 2 80 S C A F V V L M A H 2 82 A F V V L M A HG R 2 87 M A H G R E G F L K 2 89 H G R E G F L K G E 2 90 G R E G F L KG E D 2 91 R E G F L K G E D G 2 95 L K G E D G E M V K 2 104 K L E N LF E A L N 2 105 L E N L F E A L N N 2 112 L N N K N C Q A L R 2 116 N CQ A L R A K P K 2 121 R A K P K V Y I I Q 2 128 I I Q A C R G E Q R 2129 I Q A C R G E Q R D 2 132 C R G E Q R D P G E 2 161 T Y T D A L H VY S 2 164 D A L H V Y S T V E 2 171 T V E G Y I A Y R H 2 173 E G Y I AY R H D Q 2 188 I Q T L V D V F T K 2 189 Q T L V D V F T K R 2 203 L EL L T E V T R R 2 206 L T E V T R R M A E 2 208 E V T R R M A E A E 2213 M A E A E L V Q E G 2 217 E L V Q E G K A R K 2 224 A R K T N P E IQ S 2 1 M S N P R S L E E E 1 15 S G A R L A L I L C 1 21 L I L C V T KA R E 1 22 I L C V T K A R E G 1 23 L C V T K A R E G S 1 24 C V T K A RE G S E 1 25 V T K A R E G S E E 1 26 T K A R E G S E E D 1 31 G S E E DL D A L E 1 36 L D A L E H M F R Q 1 41 H M F R Q L R F E S 1 47 R F E ST M K R D P 1 54 R D P T A E Q F Q E 1 60 Q F Q E E L E K F Q 1 66 E K FQ Q A I D S R 1 67 K F Q Q A I D S R E 1 68 F Q Q A I D S R E D 1 81 C AF V V L M A H G 1 92 E G F L K G E D G E 1 106 E N L F E A L N N K 1 108L F E A L N N K N C 1 109 F E A L N N K N C Q 1 114 N K N C Q A L R A K1 118 Q A L R A K P K V Y 1 124 P K V Y I I Q A C R 1 125 K V Y T I Q AC R G 1 127 Y I I Q A C R G E Q 1 145 G D E I V M V I K D 1 147 E I V MV I K D S P 1 151 V I K D S P Q T I P 1 158 T I P T Y T D A L H 1 160 PT Y T D A L H V Y 1 166 L H V Y S T V E G Y 1 169 Y S T V E G Y I A Y 1170 S T V E G Y I A Y R 1 172 V E G Y I A Y R H D 1 174 G Y I A Y R H DQ K 1 175 Y I A Y R H D Q K G 1 176 I A Y R H D Q K G S 1 180 H D Q K GS C F I Q 1 190 T L V D V F T K R K 1 191 L V D V F T K R K G 1 192 V DV F T K R K G H 1 227 T N P E I Q S T L R 1 213P1F11 v.1: HLA-B*4402decamers 63 E E L E K F Q Q A I 23 100 G E M V K L E N L F 23 39 L E H MF R Q L R F 21 153 K D S P Q T I P T Y 19 157 Q T I P T Y T D A L 19 146D E I V M V I K D S 18 216 A E L V Q E G K A R 18 30 E G S E E D L D A L16 59 E Q F Q E E L E K F 16 97 G E D G E M V K L E 16 111 A L N N K N CQ A L 16 118 Q A L R A K P K V Y 16 229 P E I Q S T L R K R 16 12 Y D MS G A R L A L 15 33 E E D L D A L E H M 15 34 E D L D A L E H H F 15 186C F I Q T L V D V F 15 226 K T N P E I Q S T L 15 230 E I Q S T L R K RL 15 9 E E K Y D M S G A R 14 32 S E E D L D A L E H 14 37 D A L E H M FR Q L 14 58 A E Q F Q E E L E K 14 74 S R E D P V S C A F 14 75 R E D PV S C A F V 14 96 K G E D G E M V K L 14 103 V K L E N L F E A L 14 160P T Y T D A L H V Y 14 182 Q K G S C F I Q T L 14 196 T K R K G H I L EL 14 197 K R K G H I L E L L 14 231 I Q S T L R K R L Y 14 10 E K Y D MS G A R L 13 48 F E S T M K R D P T 13 52 M K R D P T A E Q F 13 62 Q EE L E K F Q Q A 13 77 D P V S C A F V V L 13 105 L E N L F E A L N N 13150 M V I K D S P Q T I 13 169 Y S T V E G Y I A Y 13 203 L E L L T E VT R R 13 214 A E A E L V Q E G K 13 232 Q S T L R K R L Y L 13 3 N P R SL E E E K Y 12 8 E E E K Y D M S G A 12 13 D M S G A R L A L I 12 14 M SG A R L A L I L 12 20 A L I L C V T K A R 12 65 L E K F Q Q A I D S 1285 V L M A H G R E G F 12 109 F H A L N N K N C G 12 119 A L R A K P K VY I i2 134 G E Q R D P G E T V 12 27 K A R E G S E E D L 11 29 R E G S EE D L D A 11 99 D G E M V K L E N L 11 143 V G G D E I V M V I 11 166 LH V Y S T V E G Y 11 172 V E G Y I A Y R H D 11 178 Y R H D Q K G S C F11 193 D V F T K R K G H I 11 194 V F T K R K C H I L 11 207 T E V T R RM A E A 11 209 V T R R M A E A E L 11 7 L E E E K Y D M S G 10 56 P T AE Q F Q E E L 10 86 L M A H G R E C F L 10 91 R E G F L K G E D G 10 140G E T V G G D E I V 10 220 Q E G K A R K T N P 10 120 L R A K P K V Y II 9 122 A K P K V Y I I Q A 9 139 P G E T V G G D E I 9 179 R H D Q K GS C F I 9 222 G K A R K T N P E I 9 167 H V Y S T V E G Y I 8 66 E K F QQ A I D S R 7 88 A H G R E G F L K G 7 17 A R L A L I L C V T 6 123 K PK V Y I I Q A C 6 136 Q R D P G E T V G G 6 204 E L L T E V T R R M 6208 E V T R R M A E A E 6 224 A R K T N P E I Q S 6 11 K Y D M S C A R LA 5 15 S G A R L A L I L C 5 16 G A R L A L I L C V 5 28 A R E G S E E DL D 5 38 A L E H M F R Q L R 5 40 E H M F R Q L R F E 5 50 S T M K R D PT A E 5 53 K R D P T A E Q F Q 5 71 A I D S R E D P V S 5 76 E D P V S CA F V V 5 82 A F V V L M A H G R 5 92 E G F L K G E D G E 5 106 E N L FE A L N N K 5 107 N L F E A L N N K N 5 110 E A L N N K N C Q A 5 14 N KN C 0 A L R A K 5 131 A C R G E Q R D P G 5 141 E T V G G D E I V M 5142 T V G G D E I V M V S 165 A L H V Y S T V E G 5 185 S C F I Q T L VD V 5 200 C H I L E L L T E V 5 219 V Q E G K A R K T N 5 233 S T L R KR L Y L Q 5 1 M S N P R S L E E E 4 4 P R S L E E E K Y D 4 41 H M F R QL R F E S 4 46 L R F E S T M K R D 4 70 Q A I D S R E D P V 4 72 I D S RE D P V S C 4 78 P V S C A F V V L M 4 80 S C A F V V L M A H 4 113 N NK N C Q A L R A 4 116 N C Q A L R A K P K 4 121 R A K P K V Y I I Q 4126 V Y I I Q A C R G E 4 127 Y I I Q A C R G E Q 4 135 E Q R D P G E TV G 4 155 S P Q T I P T Y T D 4 177 S T V E G Y I A Y R 4 173 E G Y I AY R H D Q 4 174 G Y I A Y R H D Q K 4 181 D Q K G S C F I Q T 4 190 T LV D V F T K R K 4 199 K G H I L E L L T E 4 215 E A E L V Q E G K A 4221 E G K A R K T N P E 4 225 R K T N P E I Q S T 4 2 S N P R S L E E EK 3 18 R L A L I L C V T K 3 19 L A L I L C V T K A 3 49 E S T M K R D PT A 3 54 R D P T A E Q F Q E 3 89 H G R E G F L K G E 3 98 E D G E M V KL E N 3 101 E M V K L E N L F E 3 104 K L E N L F E A L N 3 115 K N C QA L R A K P 3 137 R D P G E T V G G D 3 145 G D E I V M V I K D 3 152 IK D S P Q T I P T 3 158 T I P T Y T D A L H 3 176 I A Y R H D Q K G S 3177 A Y R H D Q K G S C 3 183 K G S C F I Q T L V 3 184 G S C F I Q T LV D 3 188 I Q T L V D V F T K 3 189 Q T L V D V F T K R 3 191 L V D V FT K R K G 3 192 V D V F T K R K G H 3 195 F T K R K G H I L E 3 201 H IL E L L T E V T 3 202 I L E L L T E V T R 3 206 L T E V T R R M A E 3211 R R M A E A E L V Q 3 212 R M A E A E L V Q E 3 218 L V Q E G K A RK T 3 228 N P E I Q S T L R K 3 22 I L C V T K A R E G 2 23 L C V T K AR E G S 2 43 F R Q L R F E S T M 2 44 R Q L R F E S T H K 2 45 Q L R F ES T M K R 2 51 T M K R D P T A E Q 2 60 Q F Q E E L E K F Q 2 64 E L E KF Q Q A I D 2 79 V S C A F V V L M A 2 81 C A F V V L M A H G 2 84 V V LM A H G R E G 2 87 M A H G R E G F L K 2 102 M V K L E N L F E A 2 108 LF E A L N N K N C 2 117 C Q A L R A K P K V 2 125 K V Y I I Q A C R G 2130 Q A C R G E Q R D P 2 144 G G D E I V M V I K 2 147 E I V M V I K DS P 2 154 D S P Q T I P T Y T 2 159 I P T Y T D A L H V 2 161 T Y T D AL H V Y S 2 162 Y T D A L H V Y S T 2 163 T D A L H V Y S T V 2 164 D AL H V Y S T V E 2 168 V Y S T V E G Y I A 2 171 T V E G Y I A Y R H 2187 F I Q T L V D V F T 2 198 R K G H I L E L L T 2 205 L L T E V T R RM A 2 210 T R R M A E A E L V 2 217 E L V Q E G K A R K 2 223 K A R K TN P E I Q 2 227 T N P E I Q S T L R 2 5 R S L E E E K Y D M 1 6 S L E EE K Y D M S 1 21 L I L C V T K A R E 1 26 T K A R E G S E E D 1 31 G S EE D L D A L E 1 35 D L D A L E H M F R 1 36 L D A L E H M K R Q 1 42 M FR Q L R F E S T 1 47 R F E S T M K R D P 1 55 D P T A E Q F Q E E 1 57 TA E Q F Q E E L E 1 61 F Q E E L E K F Q Q 1 67 K F Q Q A I D S R E 1 68F Q Q A I D S R E D 1 69 Q Q A I D S R E D P 1 73 D S R E D P V S C A 183 F V V L M A H G R E 1 90 G R E G F L K G E D 1 93 G F L K G E D G E M1 94 F L K G E D G E M V 1 95 L K G E D G E M V K 1 112 L N N K N C Q AL R 1 128 I I Q A C R G E Q R 1 133 R G E Q R D P G E T 1 148 I V M V IK D S P Q 1 149 V M V I K D S P Q T 1 151 V I K D S P Q T I P 1 175 Y IA Y R H D Q K G 1 213 M A E A TABLE XIXB, part 2: MHC Class I decameranalysis of 213P1F11 v.2 (aa 1-230). 213P1511 v.2: HLA-A*0201 decamers52 W M C S R R G K D I 15 18 Y L P S E A P P N P 13 38 T D M I R K A H AL 13 46 A L S R P W W M C S 12 10 P T P F Q D P L Y L 11 39 D M I R KA H A L S 11 40 M I R K A H A L S R 11 13 F Q D P L Y L P S E 10 16 P LY L P S E A P P 10 28 P L W N S Q D T S P 10 32 S Q D T S P T D M I 1035 T S P T D M I R K A 10 2 H V Y S T V E G P T 9 5 S T V E G P T P F Q9 44 A H A L S R P W W M 8 55 S R R G K D I S W N 8 8 E G P T P F Q D PL 7 17 L Y L P S E A P P N 7 20 P S E A P P N P P L 7 21 S E A P P N P PL W 7 29 L W N S Q D T S P T 7 37 P T D M I R K A H A 7 1 L H V Y S T VE G P 6 11 T P F Q D P L Y L P 6 4 Q D P L Y L P S E A 6 23 A P P N PP L W N S 6 43 K A H A L S R P W W 6 45 H A L S R P W W M C 6 47 L S R PW W M C S R 6 6 T V E G P T P F Q D 5 19 L P S E A P P N P P 5 31 N S QD T S P T D M 5 34 D T S P T D M I R K 5 41 I R K A H A L S R P 5 3 V YS T V E G P T P 4 22 E A P P N P P L W N 4 26 N P P L W N S Q D T 4 7 VE G P T P F Q D P 3 9 G P T P F Q D P L Y 3 24 P P N P P L W N S Q 3 30W N S Q D T S P T D 3 51 W W M C S R R G K D 3 36 S P T D M I R K A H 242 R K A H A L S R P W 2 48 S R P W W M C S R R 2 54 C S R R G K D I S W2 4 Y S T V E G P T P F 1 15 D P L Y L P S E A P 1 27 P P L W N S Q D TS 1 49 R P W W M C S R R G 1 12 P F Q D P L Y L P S −1 25 P N P P L W NS Q D −1 33 Q D T S P T D M I R −1 213P1F11 v.2: HLA-A*0202 decamers 44A H A L S R P W W M 4 21 S E A P P N P P L W 3 42 R K A H A L S R P W 322 E A P P N P P L W N 2 43 K A H A L S R P W W 2 45 H A L S R P W W M C2 23 A P P N P P L W N S 1 46 A L S R P W W M C S 1 213P1411 v2:HLA-A*0203 decamers 37 P T D M I R K A H A 18 14 Q D P L Y L P S E A 1035 T S P T D M I R K A 10 15 D P L Y L P S E A P 9 36 S P T D M I R K AH 9 38 T D M I R K A H A L 9 16 P L Y L P S E A P P 8 39 D M I R K A H AL S 8 213P1F11 v.2: HLA-A1 decamers 9 G P T P F Q D P L Y 21 37 P T D MI R K A H A 16 13 F Q D P L Y L P S E 15 20 P S E A P P N P P L 15 34 DT S P T D M I R K 14 32 S Q D T S P T D M T 13 10 P T P F Q D P L Y L 126 T V E G P T P F Q D 11 22 E A P P N P P L W N 10 5 S T V E G P T P F Q8 7 V E G P T P F Q D P 8 21 S E A P P N P P L W 8 47 L S R P W W M C SR 8 54 C S R R G K D I S W 8 4 Y S T V E G P T P F 6 12 P F Q D P L Y LP S 6 35 T S P T D M I R K A 6 40 M I R K A H A L S R 6 25 P N P P L WN S Q D 5 17 L Y L P S E A P P N 4 24 P P N P P L W N S Q 4 31 N S Q D TS P T D M 4 18 Y L P S E A P P N P 3 36 S P T D M I R K A H 3 51 W W M CS R R G K D 3 55 S R R G K D I S W N 3 3 V Y S T V E G P T P 2 11 T P FQ D P L Y L P 2 39 D M I R K A H A L S 2 46 A L S R P W W M C S 2 48 SR P W W M C S R R 2 1 L H V Y S T V E G P 1 16 P L Y L P S E A P P 1 23A P P N P P L W N S 1 28 P L W N S Q D T S P 1 43 K A H A L S R P W W 144 A H A L S R P W W M 1 45 H A L S R P W W M C 1 50 P W W M C S R R G K1 52 W M C S R R G K D I 1 213P1F11 v.2: HLA-A26 decamers 34 D T S P T DM I R K 23 10 P T P F Q D P L Y L 19 8 E G P T P F Q D P L 15 5 S T V EG P T P F Q 13 6 T V E G P T P F Q D 13 9 G P T P F Q D P L Y 13 37 PT D M I R K A H A 13 18 Y L P S E A P P N P 12 40 M I R K A H A L S R 1256 R R G K D I S W N F 12 2 H V Y S T V E G P T 11 12 P F Q D P L Y L PS 11 4 Y S T V E G P T P F 10 13 F Q D P L Y L P S E 9 16 P L Y L P SE A P P 9 20 P S E A P P N P P L 9 22 E A P P N P P L W N 9 28 P L W N SQ D T S P 9 31 N S Q D T S P T D M 9 38 T D M I R K A H A L 9 39 D M I RK A H A L S 9 44 A H A L S R P W W M 9 46 A L S R P W W M C S 9 7 V E GP T P F Q D P 7 11 T P F Q D P L Y L P 7 15 D P L Y L P S E A P 7 41 I RK A H A L S R P 7 47 L S R P W W M C S R 7 55 S R R G K D I S W N 7 23 AP P N P P L W N S 6 35 T S P T D M I R K A 6 1 L H V Y S T V E G P 5 25P N P P L W N S Q D 5 21 S E A P P N P P L W 4 14 Q D P L Y L P S E A 317 L Y L P S E A P P N 3 24 P P N P P L W N S Q 3 48 S R P W W M C S R R3 19 L P S E A P P N P P 2 26 N P P L W N S Q D T 2 29 L W N S Q D T S PT 2 30 W N S Q D T S P T D 2 32 S Q D T S P T D M I 2 33 Q D T S P T D MI R 2 36 S P T D M I R K A H 2 45 H A L S R P W W M C 2 3 V Y S T V E GP T P 1 42 R K A H A L S R P W 1 43 K A H A L S R P W W 1 49 R P W W M CS R R G 1 50 P W W M C S R R G K 1 51 W W M C S R R G K D 1 52 W M C S RR G K D I 1 54 C S R R G K D I S W 1 213P1F11 v.2: HLA-A3 decamers 40 MI R K A H A L S R 23 16 P L Y L P S E A P P 18 46 A L S R P W W M C S 176 T V E G P T P F Q D 16 2 H V Y S T V E G P T 15 28 P L W N S Q D T S P14 34 D T S P T D M I R K 13 47 L S R P W W M C S R 12 18 Y L P S EA P P N P 11 50 P W W M C S R R G K 11 55 S R R G K D I S W N 10 9 G PT P F Q D P L Y 9 25 P N P P L W N S Q D 9 39 D M I R K A H A L S 9 17 LY L P S E A P P N 8 22 E A P P N P P L W N 8 36 S P T D M I R K A H 8 41I R K A H A L S R P 8 48 S R P W W M C S R R 8 54 C S R R C K D I S W 856 R R G K D I S W N F 8 3 V Y S T V E G P T P 7 14 Q D P L Y L P S E A7 33 Q D T S P T D M I R 7 43 K A H A L S R P W W 7 44 A H A L S R P W WM 7 4 Y S T V E G P T P F 6 21 S E A P P N P P L W 6 27 P P L W N S Q DT S 6 13 F Q D P L Y L P S E 5 24 P P N P P L W N S Q 5 38 T D M I RK A H A L 5 42 R K A H A L S R P W 5 10 P T P F Q D P L Y L 4 12 P F Q DP L Y L P S 4 23 A P P N P P L W N S 4 30 W N S Q D T S P T D 4 49 R PW W M C S R R G 4 7 V E G P T P F Q D P 3 15 D P L Y L P S E A P 3 29 LW N S Q D T S P T 3 31 N S Q D T S P T D M 3 37 P T D M I R K A H A 3 45H A L S R P W W N C 3 52 W M C S R R G K D I 3 53 M C S R R G K D I S 35 S T V E G P T P F Q 2 19 L P S E A P P N P P 2 20 P S E A P P N P P L2 32 S Q D T S P T D M I 2 51 W W M C S R R G K D 2 26 N P P L W N S Q DT 1 213P1F11 v.2 HLA-B*0702 decamers 26 N P P L W N S Q D T 16 19 L P SE A P P N P P 13 20 P S E A P P N P P L 13 8 E G P T P F Q D P L 12 9 GP T P F Q D P L Y 12 10 P T P F Q D P L Y L 12 23 A P P N P P L W N S 1236 S P T D M I R K A H 12 38 T D M I R K A H A L 12 15 D P L Y L P S E AP 11 24 P P N P P L W N S Q 11 49 R P W W M C S R R C 11 11 T P F Q D PL Y L P 10 27 P P L W N S Q D T S 10 44 A H A L S R P W W M 9 56 R R G KD I S W N F 9 4 Y S T V E G P T P F 8 29 L W N S Q D T S P T 8 32 S Q DT S P T D H I 8 37 P T D M I R K A H A 8 2 H V Y S T V E G P T 7 31 N SQ D T S P T D M 7 14 Q D P L Y L P S E A 6 35 T S P T D M I R K A 6 52 WM C S R R G K D I 6 40 M I R K A H A L S R 5 22 E A P P N P P L W N 4 43K A H A L S R P W W 4 46 A L S R P W W M C S 4 55 S R R G K D I S W N 43 V Y S T V E G P T P 3 5 S T V E G P T P F Q 3 7 V E G P T P F Q D P 312 P F Q D P L Y L P S 3 13 F Q D P L Y L P S E 3 17 L Y L P S E A P P N3 21 S E A P P N P P L W 3 30 W N S Q D T S P T D 3 34 D T S P T D M I RK 3 42 R K A H A L S R P W 3 47 L S R P W W M C S R 3 6 T V E G P T P FQ D 2 16 P L Y L P S E A P P 2 41 T R K A H A L S R P 2 51 W W M C S R RG K D 2 53 M C S R R G K D I S 2 54 C S R R G K D I S W 2 1 L H V Y S TV E G P 1 18 Y L P S E A P P N P 1 25 P N P P L W N S Q D 1 28 P L W N SQ D T S P 1 39 D M I R K A H A L S I 50 P W W M C S R R G K 1 213P1F11v.2: HLA-B*4402 decamers 21 S E A P P N P P L W 26 38 T D M I R K A H AL 15 7 V E G P T P F Q D P 14 8 E G P T P F Q D P L 14 9 G P T P F Q D PL Y 14 10 P T P F Q D P L Y L 13 32 S Q D T S P T D M I 12 43 K A H A LS R P W W 12 54 C S R R G K D I S W 12 4 Y S T V E G P T P F 11 42 R K AH A L S R P W 11 20 P S E A P P N P P L 10 52 W M C S R R G K D I 10 56R R G K D I S W N F 10 22 E A P P N P P L W N 8 35 T S P T D M I R K A 736 S P T D M I R K A H 7 23 A P P N P P L W N S 6 13 F Q D P L Y L P S E5 17 L Y L P S E A P P N 5 25 P N P P L W N S Q D 5 34 D T S P T D M I RK 5 39 D M I R K A H A L S 5 44 A H A L S R P W W M 5 46 A L S R P W W MC S 5 55 S R R G K D I S W N 5 11 T P F Q D P L Y L P 4 24 P P N P P L WN S Q 4 3 V Y S T V E G P T P 3 6 T V E G P T P F Q D 3 14 Q D P L Y L PS E A 3 15 D P L Y L P S E A P 3 19 L P S E A P P N P P 3 26 N P P L W MS Q D T 3 31 N S Q D T S P T D M 3 47 L S R P W W M C S R 3 51 W W M C SR R G K D 3 5 S T V E G P T P F Q 2 12 P F Q D P L Y L P S 2 18 Y L P SE A P P N P 2 27 P P L W N S Q D T S 2 30 W N S Q D T S P T D 2 40 M I RK A H A L S R 2 48 S R P W W M C S R R 2 50 P W W M C S R R G K 2 53 M CS R R G K D I S 2 TABLE XIXB, part 3: MHC Class I decamer analysis of213P1F11 v.3 (aa 1-146). 213P1F11 v.3: HLA-A*0201 decamers 3 I I Q A CR G A T L 24 10 A T L P S P F P Y L 21 2 Y I I Q A C R G A T 17 12 L P SP F P Y L S L 17 6 A C R G A T L P S P 11 11 T L P S P F P Y L S 11 1 VY I I Q A C R G A 8 5 Q A C R G A T L P S 5 4 I Q A C R G A T L P 4 9 GA T L P S P F P Y 4 8 R G A T L P S P F P 3 213P1F11 v.3: HLA-A*0202decamers 4 I Q A C R G A T L P 3 8 R G A T L P S P F P 3 5 Q A C R G A TL P S 2 9 G A T L P S P F P Y 2 6 A C R G A T L P S P 1 10 A T L P S P FP Y L 1 213P1511 v.3: HLA-A*0203 decamers 1 V Y I I Q A C R G A 10 2 YI I Q A C R G A T 9 3 I I Q A C R G A T L 8 213P1511 v.3: HLA-A1decamers 9 G A T L P S P F P Y 15 10 A T L P S P F P Y L 14 12 L P S P FP Y L S L 10 5 Q A C R G A T L P S 6 2 Y I I Q A C R G A T 3 11 T L P SP F P Y L S 3 4 I Q A C R G A T L P 2 6 A C R G A T L P S P 2 1 V Y I IQ A C R G A 1 3 I I Q A C R C A T L 1 213P1F11 v.3: HLA-A26 decamers 10A T L P S P F P Y L 25 3 I I Q A C R C A T L 19 12 L P S P F P Y L S L15 2 Y I I Q A C R C A T 1 7 C R C A T L P S P F 11 9 G A T L P S P F PY 1 11 T L P S P F P Y L S 1 6 A C R C A T L P S P 8 1 V Y I I Q A C R CA 3 8 R C A T L P S P F P 2 4 I Q A C R G A T L P 1 213P1F11 v.3: HLA-A3decamers 3 I I Q A C R G A T L 22 2 Y I I Q A C R G A T 14 11 T L P S PF P Y L S 11 6 A C R G A T L P S P 1 7 C R G A T L P S P F 1 5 Q A C R CA T L P S 8 9 G A T L P S P F P Y 8 10 A T L P S P F P Y L 8 12 L P S PF P Y L S L 8 4 I Q A C R G A T L P 7 8 R G A T L P S P F P 5 1 V Y I IQ A C R G A 4 213P1F11 v.3: HLA-B*0702 decamers 12 L P S P F P Y L S L25 10 A T L P S P F P Y L 15 3 I I Q A C R G A T L 13 7 C R G A T L P SP F 9 2 Y I I Q A C R G A T 8 6 A C R C A T L P S P 7 1 V Y I I Q A C RG A 6 5 Q A C R C A T L P S 4 8 R G A T L P S P F P 4 4 I Q A C R G A TL P 3 TABLE XIXB, part 4: MHC Class I decamer analysis of 213P1F11 v.4(aa 1-321). 213P1F11 v.4: HLA-A*0201 decamers 12 S V Q P E K R T G L 1960 E V F G G G V C D I 16 65 G V G D I V G R D L 16 10 S L S V Q P E K RT 15 52 V N D P R E T Q E V 15 57 E T Q E V F G C G V 14 67 G D I V CR D L S I 14 42 F R G S S V H Q K L 13 50 K L V N D P R E T Q 13 61 V FC C C V G D I V 13 68 D I V C R D L S I S 13 84 S A S E E E K Y D M 13 2G K C Q E Y D K S L 12 20 G L R D E N G E C G 12 33 R L K E E Q C R A F12 38 Q G R A F R C S S V 12 73 D L S I S F R N S E 12 4 C Q E Y D K S LS V 11 46 S V H Q K L V N D P 11 75 S I S F R N S E T S 11 74 L S I S FR N S E T 10 25 N G E C G Q T F R L 9 41 A F R G S S V H Q K 9 43 R G SS V H Q K L V 9 76 I S F R N S E T S A 9 45 S S V H Q K L V N D 8 49 Q KL V N D P R E T 8 213P1F11 v.4: HLA-A*0201 decamers 51 L V N D P R E T QE 8 63 G G G V G D I V G R 8 69 I V G R D L S T S F 8 32 F R L K E E Q GR A 7 40 R A F R G S S V H Q 7 64 G G V G D I V G R D 7 5 Q E Y D K S LS V Q 6 18 R T G L R D E N G E 6 70 V G R D L S I S F R 6 78 F R N S ET S A S E 6 7 Y D K S L S V Q P E 5 9 K S L S V Q P E K R 5 21 L R D E NG E C G Q 5 28 C G Q T F R L K E E 5 30 Q T F R L K E E Q G 5 34 L K E EQ G R A F R 5 86 S E E E K Y D M S G 5 11 L S V Q P E K R T G 4 19 T G LR D E N G E C 4 23 D E N G E C G Q T F 4 79 R N S E T S A S E E 4 3 K CQ E Y D K S L S 3 13 V Q P E K R T G L R 3 22 R D E N G E C G Q T 3 26 GE C G Q T F R L K 3 54 D P R E T Q E V F G 3 62 F G G G V G D I V G 3 77S F R N S E T S A S 3 81 S E T S A S E E E K 3 82 E T S A S E E E K Y 385 A S E E E K Y D M S 3 8 D K S L S V Q P E K 2 17 K R T G L R D E N G2 39 G R A F R G S S V H 2 44 G S S V H Q K L V N 2 59 Q E V F G G G V GD 2 72 R D L S I S F R N S 2 1 M G K C Q E Y D K S 1 29 G Q T F R L K EE Q 1 31 T F R L K E E Q G R 1 47 V H Q K L V N D P R 1 55 P R E T Q E VF G G 1 66 V G D I V G R D L S 1 71 G R D L S I S F R N 1 80 N S E T SA S E E E 1 83 T S A S E E E K Y D 1 6 E Y D K S L S V Q P −1 16 E K R TG L R D E N −1 24 E N G E C G Q T F R −1 37 E Q G R A F R G S S −1 58 TQ E V F G G G V G −1 213P1F11 v.4: HLA-A*0202 decamers 39 G R A F R G SS V H 3 83 T S A S E E E K Y D 3 40 R A F R G S S V H Q 2 84 S A S E E EK Y D M 2 41 A F R G S S V H Q K 1 85 A S E E E K Y D M S 1 213P1F11v.4: HLA-A*0203 decamers 32 F R L K E E Q G R A 10 76 I S F R N S E T SA 10 33 R L K E E Q G R A F 9 77 S F R N S E T S A S 9 34 L K E E Q GR A F R 8 78 F R N S E T S A S E 8 213P1F11 v.4: HLA-A1 decamers 82 ET S A S E E E K Y 23 14 Q P E K R T G L R D 17 4 C Q E Y D K S L S V 1685 A S E E E K Y D M S 16 52 V N D P R E T Q E V 15 66 V G D I V G R D LS 14 86 N S E T S A S E E E 14 58 T Q E V F G G G V G 12 86 S E E E K YD M S G 12 34 L K E E Q G R A F R 11 44 G S S V H Q K L V N 11 55 P R ET Q E V F G G 11 6 E Y D K S L S V Q P 10 21 L R D E N G E C G Q 10 22 RD E N G E C G Q T 10 25 N G E C G Q T F R L 10 35 K E E Q G R A F R G 1071 G R D L S I S F R N 10 27 E C G Q T F R L K E 9 12 S V Q P E K R T GL 7 57 E T Q E V F G G G V 7 62 F G G G V G D I V G 7 9 K S L S V Q P EK R 6 18 R T G L R D E N G E 6 26 G E C G Q T F R L K 6 30 Q T F R L KE E Q G 6 45 S S V H Q K L V N D 6 67 G D I V G R D L S I 6 74 L S I S FR N S E T 5 11 L S V Q P E K R T G 4 36 E E Q G R A F R G S 4 69 I V G RD L S I S F 4 76 I S F R N S E T S A 4 83 T S A S E E E K Y D 4 7 Y D KS L S V Q P E 3 10 S L S V Q P E K R T 3 13 V Q P E K R T G L R 3 41 AF R G S S V H Q K 3 42 F R G S S V H Q K L 3 46 S V H Q K L V N D P 3 56R E T Q E V F G G G 3 61 V F G G G V G D I V 3 72 R D L S I S F R N S 31 M G K C Q E Y D K S 2 3 K C Q E Y D K S L S 2 20 G L R D E N G E C G 223 D E N G E C G Q T F 2 33 R L K E E Q G R A F 2 43 R G S S V H Q K L V2 47 V H Q K L V N D P R 2 50 K L V N D P R E T Q 2 60 E V F G G G V G DI 2 64 G G V G D I V G R D 2 73 D L S I S F R N S E 2 75 S I S F R N S ET S 2 77 S F R N S E T S A S 2 81 S E T S A S E E E K 2 84 S A S E E EK Y D M 2 5 Q E Y D K S L S V Q 1 16 E K R T G L R D E N 1 17 K R T G LR D E N G 1 19 T G L R D E N G E C 1 32 F R L K E E Q G R A 1 37 E Q G RA F R G S S 1 38 Q G R A F R G S S V 1 39 G R A F R G S S V H 1 53 N D PR E T Q E V F 1 59 Q E V F G G G V G D 1 65 G V G D I V G R D L 1 68 DI V G R D L S I S 1 70 V G R D L S I S F R 1 78 F R N S E T S A S E 1213P1F11 v.4: HLA-A26 decamers 82 E T S A S E E E K Y 27 60 E V F G G GV G D I 24 68 D I V G R D L S I S 23 33 R L K E E Q G R A F 22 12 S V QP E K R T G L 21 69 I V G R D L S I S F 21 23 D E N G E C G Q T F 19 57E T Q E V F G G G V 19 65 G V G D I V G R D L 19 46 S V H Q K L V N D P15 73 D L S I S F R N S E 15 30 Q T F R L K E E Q G 13 36 E E Q G R A FR G S 13 41 A F R G S S V H Q K 13 51 L V N D P R E T Q E 12 18 R T G LR D E N G E 11 42 F R G S S V H Q K L 11 53 N D P R E T Q E V F 11 2 G KC Q E Y D K S L 10 6 E Y D K S L S V Q P 10 75 S I S F R N S E T S 10 84S A S E E E K Y D M 10 10 S L S V Q P E K R T 9 20 G L R D E N G E C G 925 N G E C G Q T F R L 9 54 D P R E T Q E V F G 9 8 D K S L S V Q P E K8 24 E N G E C G Q T F R 8 27 E C G Q T F R L K E 8 31 T F R L K E E Q GR 8 50 K L V N D P R E T Q 8 61 V F G G G V G D I V 8 77 S F R N S E T SA S 8 7 Y D K S L S V Q P E 7 16 E K R T G L R D E N 7 37 E Q G R A F RG S S 7 64 G G V G D I V G R D 7 85 A S E E E K Y D M S 7 1 M G K C Q EY D K S 6 5 Q E Y D K S L S V Q 6 26 G E C G Q T F R L K 6 45 S S V H QK L V N D 6 56 R E T Q E V F G G G 6 63 G G G V G D I V G R 6 70 V G R DL S I S F R 6 72 R D L S I S F R N S 6 15 P E K R T G L R D E 5 28 C G QT F R L K E E 5 52 V N D P R E T Q E V 5 55 P R E T Q E V F G G 5 74 L SI S F R N S E T 5 21 L R D E N G E C G Q 4 40 R A F R G S S V H Q 4 79 RN S E T S A S E E 4 86 S E E E K Y D M S G 4 3 K C Q E Y D K S L S 3 13V Q P E K R T G L R 3 17 K R T G L R D E N G 3 34 L K E E Q G R A F R 348 H Q K L V N D P R E 3 67 G D I V G R D L S I 3 76 I S F R N S E T S A3 78 F R N S E T S A S E 3 9 K S L S V Q P E K R 2 14 Q P E K R T G L RD 2 32 F R L K E E Q G R A 2 35 K E E Q G R A F R G 2 38 Q G R A F R G SS V 2 39 G R A F R G S S V H 2 59 Q E V F G G G V G D 2 62 F G G G V G DI V G 2 71 G R D L S I S F R N 2 81 S E T S A S E E E K 2 83 T S A S E EE K Y D 2 4 C Q E Y D K S L S V 1 11 L S V Q P E K R T G 1 19 T G L R DE N G E C 1 22 R D E N G E C G Q T 1 29 G Q T F R L K E E Q 1 43 R G S SV H Q K L V 1 47 V H Q K L V N D P R 1 49 Q K L V N D P R E T 1 66 V G DT V G R D L S 1 80 N S E T S A S E E E 1 213P1F11 v.4: HLA-A3 decamers33 R L K E E Q G R A F 24 41 A F R C S S V H Q K 21 69 I V G R D L S I SF 21 50 K L V N D P R E T Q 19 20 G L R D E N G E C G 17 12 S V Q P EK R T G L 16 38 Q G R A F R G S S V 15 51 L V N D P R E T Q E 15 5 Q EY D K S L S V Q 14 65 G V G D I V G R D L 14 73 D L S I S F R N S E 1423 D E N G E C G Q T F 13 60 E V F G G G V G D T 13 68 D I V G R D L S IS 13 75 S I S F R N S E T S 13 26 G E C G Q T F R L K 12 39 G R A F RG S S V H 12 8 D K S L S V Q P E K 11 10 S L S V Q P E K R T 11 40 R AF R G S S V H Q 11 46 S V H Q K L V N D P 11 53 N D P R E T Q E V F 1170 V G R D L S I S F R 11 79 R N S E T S A S E E 11 81 S E T S A S E E EK 11 9 K S L S V Q P E K R 10 22 R D E N G E C G Q T 9 34 L K E E QG R A F R 9 59 Q E V F G G G V G D 9 77 S F R N S E T S A S 9 14 Q P E KR T G L R D 8 30 Q T F R L K E E Q G 8 31 T F R L K E E Q G R 8 54 D PR E T Q E V F G 8 58 T Q E V F G G G V G 8 63 G G G V G D I V G R 8 67 GD I V G R D L S I 8 76 I S F R N S E T S A 8 82 E T S A S E E E K Y 8 3K C Q E Y D K S L S 7 6 E Y D K S L S V Q P 7 37 E Q G R A F R G S S 744 G S S V H Q K L V N 7 13 V Q P E K R T G L R 6 19 T G L R D E N G E C6 24 E N G E C G Q T F R 6 35 K E E Q G R A F R G 6 62 F G G G V G D I VG 6 72 R D L S I S F R N S 6 74 L S I S F R N S E T 6 4 C Q E Y D K S LS V 5 17 K R T G L R D E N G 5 18 R T G L R D E N G E 5 45 S S V H QK L V N D 5 49 Q K L V N D P R E T 5 56 R E T Q E V F G G G 5 57 E T Q EV F G G G V 5 61 V F G G G V G D I V 5 78 F R N S E T S A S E 5 85 A SE E E K Y D M S 5 86 S E E E K Y D M S G 5 11 L S V Q P E K R T G 4 15 PE K R T G L R D E 4 16 E K R T G L R D E N 4 27 E C G Q T F R L K E 4 43R G S S V H Q K L V 4 47 V H Q K L V N D P R 4 32 F R L K E E Q G R A 352 V N D P R E T Q E V 3 64 G G V G D I V G R D 3 2 G K C Q E Y D K S L2 36 E E Q G R A F R G S 2 48 H Q K L V N D P R E 2 66 V G D I V G R D LS 2 84 S A S E E E K Y D M 2 1 M G K C Q E Y D K S 1 7 Y D K S L S V Q PE 1 21 L R D E N G E C G Q 1 71 G R D L S I S F R N 1 83 T S A S E E E KY D 1 213P1F11 v.4: HLA-B*0702 decamers 54 D P R E T Q E V F G 15 12 S VQ P E K R T G L 13 14 Q P E K R T G L R D 13 25 N G E C G Q T F R L 1142 F R G S S V H Q K L 11 65 G V G D I V C R D L 11 2 G K C Q E Y D K SL 10 60 E V F C G G V G D I 10 38 Q G R A F R C S S V 9 43 R G S S V H QK L V 9 52 V N D P R E T Q E V 9 61 V F G G G V G D I V 9 4 C Q E Y D KS L S V 8 10 S L S V Q P E K R T 8 23 D E N G E C G Q T F 8 33 R L K E EQ G R A F 8 67 G D I V G R D L S I 8 69 I V G R D L S I S F 8 76 I S F RN S E T S A 8 84 S A S E E E K Y D M 8 22 R D E N G E C G Q T 7 32 F R LK E E Q G R A 7 41 A F R G S S V H Q K 7 53 N D P R E T Q E V F 7 57 E TQ E V F C G G V 7 49 Q K L V N D P R E T 6 74 L S I S F R N S E T 6 6 EY D K S L S V Q P 5 27 E C G Q T F R L K E 5 44 G S S V H Q K L V N 5 16E K R T G L R D E N 4 24 E N C E C G Q T F R 4 36 E E Q C R A F R G S 462 F G G G V G D I V C 4 77 S F R N S E T S A S 4 82 E T S A S E E E K Y4 8 D K S L S V Q P E K 3 17 K R T G L R D E N G 3 26 C E C G Q T F R LK 3 34 L K E E Q G R A F R 3 37 E Q G R A F R G S S 3 40 R A F R G S S VH Q 3 63 G G G V G D I V G R 3 64 C G V G D I V G R D 3 70 V G R D L S IS F R 3 73 D L S I S F R N S E 3 79 R N S E T S A S E E 3 7 Y D K S L SV Q P E 2 18 R T C L R D E N G E 2 20 C L R D E N G E C C 2 31 T F R L KE E Q G R 2 39 G R A F R G S S V H 2 45 S S V H Q K L V N D 2 47 V H Q KL V N D P R 2 50 K L V N D P R E T Q 2 56 R E T Q E V F G G G 2 59 Q E VF C G G V G D 2 66 V G D I V G R D L S 2 68 D I V C R D L S I S 2 72 R DL S I S F R N S 2 75 S I S F R N S E T S 2 85 A S E E E K Y D M S 2 3 KC Q E Y D K S L S 1 5 Q E Y D K S L S V Q 1 9 K S L S V Q P E K R 1 13 VQ P E K R T G L R 1 21 L R D E N G E C G Q 1 35 K E E Q G R A F R G 1 46S V H Q K L V N D P 1 48 H Q K L V N D P R E 1 51 L V N D P R E T Q E 155 P R E T Q E V F G G 1 58 T Q E V F G G G V G 1 71 G R D L S I S F R N1 78 F R N S E T S A S E 1 83 T S A S E E E K Y D 1 213P1F11 v.4:HLA-B*4402 decamers 23 D E N G E C G Q T F 22 12 S V Q P E K R T G L 1536 E E Q G R A F R G S 15 26 G E C G Q T F R L K 14 53 N D P R E T Q E VF 14 60 E V F G G G V G D I 14 82 E T S A S E E E K Y 14 5 Q E Y D K S LS V Q 13 15 P E K R T G L R D E 13 33 R L K E E Q G R A F 13 2 G K C Q EY D K S L 12 25 N G E C G Q T F R L 12 35 K E E Q G R A F R G 12 65 G VG D I V G R D L 12 67 G D I V C R D L S I 12 69 I V G R D L S I S F 1242 F R C S S V H Q K L 11 56 R E T Q E V F C G G 11 59 Q E V F C G G V GD 11 81 S E T S A S E E E K 11 86 S E E E K Y D M S G 11 41 A F R C S SV H Q K 7 6 E Y D K S L S V Q P 5 27 E C C Q T F R L K E 5 52 V N D P RE T Q E V 5 77 S F R N S E T S A S 5 9 K S L S V Q P E K R 4 10 S L S VQ P E K R T 4 16 E K R T G L R D E N 4 28 C G Q T F R L K E E 4 30 Q T FR L K E E Q G 4 37 E Q G R A F R G S S 4 40 R A F R G S S V H Q 4 43 R GS S V H Q K L V 4 50 K L V N D P R E T Q 4 63 G G G V G D I V G R 4 70 VG R D L S I S F R 4 13 V Q P E K R T G L R 3 44 G S S V H Q K L V N 3 45S S V H Q K L V N D 3 46 S V H Q K L V N D P 3 49 Q K L V N D P R E T 362 F G G G V G D I V G 3 66 V G D I V G R D L S 3 72 R D L S I S F R N S3 73 D L S I S F R N S E 3 74 L S I S F R N S E T 3 75 S I S F R N S E TS 3 76 I S F R N S E T S A 3 85 A S E E E K Y D M S 3 3 K C Q E Y D K SL S 2 8 D K S L S V Q P E K 2 11 L S V Q P E K R T G 2 17 K R T G L R DE N G 2 18 R T G L R D E N G E 2 19 T G L R D E N G E C 2 22 R D E N G EC G Q T 2 24 E N G E C G Q T F R 2 51 L V N D P R E T Q E 2 55 P R E T QE V F G G 2 57 E T Q E V F G& TABLE XIXB, part 5: MHC Class I decameranalysis of 213P1511 v.5 (aa 1-242). 213P1511 v.5: HLA-A*0201 decamers 2G A R L A L I L R V 20 5 L A L I L R V T K A 18 4 R L A L I L R V T K 166 A L I L R V T K A R 14 7 L I L R V T K A R E 14 8 I L R V T K A R E G14 3 A R L A L I L R V T 12 1 S G A R L A L I L R 8 10 R V T K A R E G SE 5 9 L R V T K A R E G S 3 213P1F11 v.5: HLA-A*0202 decamers 1 S G A RL A L I L R 3 4 R L A L I L R V T K 3 2 G A R L A L I L R V 2 5 L A L IL R V T K A 2 3 A R L A L I L R V T 1 6 A L I L R V T K A R 1 213P1F11v.5: HLA-A*0203 decamers 5 L A L I L R V T K A 10 6 A L I L R V T K A R9 7 L I L R V T K A R E 8 213P1F11 v.5: HLA-A1 decamers 1 S G A R L AL I L R 8 2 G A R L A L I L R V 6 5 L A L I L R V T K A 3 3 A R L A L IL R V T 2 4 R L A L I L R V T K 2 6 A L I L R V T K A R 2 8 I L R V T KA R E G 1 9 L R V T K A R E G S 1 213P1F11 v.5: HLA-A26 decamers 7 L I LR V T K A R E 12 10 R V T K A R E G S E 12 6 A L I L R V T K A R 11 4 RL A L I L R V T K 10 8 I L R V T K A R E G 9 1 S G A R L A L I L R 5 2 GA R L A L I L R V 5 3 A R L A L I L R V T 4 9 L R V T K A R E G S 1213P1F11 v.5: HLA-A3 decamers 4 R L A L I L R V T K 35 6 A L I L R V T KA R 22 8 I L R V T K A R E G 18 10 R V T K A R E G S E 17 7 L I L R VT K A R E 16 3 A R L A L I L R V T 11 1 S G A R L A L I L R 9 2 G A R LA L I L R V 7 5 L A L I L R V T K A 4 9 L R V T K A R E G S 1 213P1F11v.5: HLA-B*0702 decamers 2 G A R L A L I L R V 10 3 A R L A L I L R V T10 5 L A L I L R V T K A 8 4 R L A L I L R V T K 5 6 A L I L R V T K A R4 8 I L R V T K A R E G 3 10 R V T K A R E G S E 2 1 S G A R L A L I L R1 7 L I L R V T K A R E 1 9 L R V T K A R E G S 1 213P1F11 v.5:HLA-B*4402 decamers 6 A L I L R V T K A R 12 3 A R L A L I L R V T 7 1 SG A R L A L I L R 5 2 G A R L A L T L R V 5 4 TABLE XIXB, part 6: MHCClass I decamer analysis of 213P1F11 v.6 (aa 1-242). 213P1F11 v.6:HLA-A*0201 decamers 9 A M N N K N C Q A L 22 5 N L F E A M N N K N 16 2K L E N L F E A M N 12 1 V K L E N L F E A M 10 8 E A M N N K N C Q A 67 F E A M N N K N C Q 4 3 L E N L F E A M N N 3 10 M N N K N C Q A L R 34 E N L F E A M N N K 1 213P1F11 v.6: HLA-A*0202 decamers 7 F E A M N NK N C Q 3 8 E A M N N K N C Q A 2 9 A M N N K N C Q A L 1 213P1F11 v.6:HLA-A*0203 decamers 8 E A M N N K N C Q A 10 1 V K L E N L F E A M 9 9 AM N N K N C Q A L 9 2 K L E N L F E A M N 8 10 M N N K N C Q A L R 8213P1F11 v.6: HLA-A1 decamers 2 K L E N L F E A M N 12 6 L F E A M N N KN C 11 1 V K L E N L F E A M 4 5 N L F E A M N N K N 4 10 M N N K N CQ A L R 2 7 F E A M N N K N C Q 1 8 E A M N N K N C Q A 1 9 A M N N K NC Q A L 1 213P1F11 v.6: HLA-A26 decamers 1 V K L E N L F E A M 15 5 N LF E A M N N K N 13 4 E N L F E A M N N K 11 2 K L E N L F E A M N 10 9 AM N N K N C Q A L 10 6 L F E A M N N K N C 7 8 E A M N N K N C Q A 7 3 LE N L F E A M N N 2 10 M N N K N C Q A L R 2 7 F E A M N N K N C Q 1213P1F11 v.6: HLA-A3 decamers 2 K L E N L F E A M N 18 4 E N L F E A M NN K 12 5 N L F E A M N N K N 11 10 M N N K N C Q A L R 7 3 L E N L FE A M N N 5 9 A M N N K N C Q A L 5 1 V K L E N L F E A M 4 8 E A M N NK N C Q A 4 6 L F E A M N N K N C 2 7 F E A M N N K N C Q 1 213P1F11v.6: HLA-B*0702 decamers 9 A M N N K N C Q A L 13 1 V K L E N L F E A M8 8 E A M N N K N C Q A 8 2 K L E N L F E A M N 2 10 M N N K N C Q A L R2 4 E N L F E A M N N K 1 6 L F E A M N N K N C 1 7 F E A M N N K N C Q1 213P1F11 v.6: HLA-B*4402 decamers 9 A M N N K N C Q A L 16 3 L E N L FE A M N N 12 7 F E A M N N K N C Q 11 5 N L F E A M N N K N 5 8 E A M NN K N C Q A 5 1 V K L E N L F E A M 4 4 E N L F E A M N N K 4 2 K L E NL F E A M N 2

[0771] TABLE XIXC MHC Class II Analysis of 213P1F11. Listed are scoreswhich correlate with the ligation strength to a defined HLA type for asequence of amino acids. The algorithms used are based on the book “MHCLigands and Peptide Motifs” by H. G. Rammensee, J. Bachmann and S.Stevanovic. The probability of being processed and presented is given inorder to predict T-cell epitopes. Pos 1 2 3 4 5 6 7 8 9 0 1 2 3 4 5score SEQ. ID NO. Table XIXC, part 1: MHC Class II 15-mer analysis of213P1F11 v.1 (aa 1-242). 213P1F11 v.1: HLA-DR B1*0101 15-mers 166 L H VY S T V E G Y I A Y R H 33 9 E E K Y D M S G A R L A I L I L 29 80 S C AF V V L M A H G R E G F 29 192 V D V F T K R K G H I L E L L 29 92 E G FL K G E D G E M V K L E 25 123 K P K V Y I I Q A C R G E Q R 25 63 E E LE K F Q Q A I D S R E D 24 145 G D E I V M V I K D S P Q T I 24 148 I VM V I K D S P Q T I P T Y 24 203 L E L L T E V T R R M A E A E 24 137 RD P G E T V G G D E I V M V 23 202 I L E L L T E V T R R M A E A 23 8 EE E K Y D M S G A R L A L I 22 39 L E H M F R Q L R F E S T M K 22 124 PK V Y I I Q A C R G E Q R D 22 176 I A Y R D Q K G S C F I Q T 22 188 IQ T L V D V F T K R K G H I 22 199 K G H I L E L L T E V T R R M 22 17 AR L A L I L C V T K A R E G 21 91 R E G F L K G E D G E M V K L 21 40 EH M F R Q L R F E S T M K R 20 99 D G E M V K L E N L F E A L N 20 208 EV T R R M A E A E L V Q E G 20 45 Q L R F E S T M K R D P T A E 19 83 FV V L M A H G R E G F L K G 19 106 E N L F E A L N N K N C Q A L 19 159I P T Y T D A L H V Y S T V E 19 43 F R Q L R F E S T M K R D P T 18 50S T M K R D P T A E Q F Q E E 18 82 A F V V L M A H G R E G F L K 18 100G E M V K L E N L F E A L N N 18 117 C Q A L R A K P K V Y I I Q A 18147 E I V M V I K D S P Q T I P T 18 149 V M V I K D S P Q T I P T Y T18 184 G S C F I Q T L V D V F T K R 18 216 A E L V Q E G K A R K T N PE 18 20 A L I L C V T K A R E G S E E 17 33 E E D L D A L E H M F R Q LR 17 69 Q Q A I D S R E D P V S C A F 17 89 H G R E G F L K G E D G E MV 17 109 F E A L N N K N C Q A L R A K 17 111 A L N N K N C Q A L R A KP K 17 114 N K N C Q A L R A K P K V I 17 140 G E T V G G D E I V M V IK D 17 157 Q T I P T Y T D A L H V Y S T 17 183 K G S C F I Q T L V D VF T K 17 200 G H I L E L L T E V T R R M A 17 206 L T E V T R R M A E AE L V Q 17 228 N P E I Q S T L R K R L Y L Q 17 4 P R S L E E E K Y D MS G A R 16 11 K Y D M S G A R L A L T L C V 16 12 Y D M S G A R L A L IL C V T 16 18 R L A L I L C V T K A R E G S 16 30 E G S E E D L D A L EH M F R 16 74 S R E D P V S C A F V V L M A 16 76 E D P V S C A F V V LM A H G 16 81 C A F V V L M A H G R E G F L 16 84 V V L M A H G R E G FL K G E 16 102 M V K L E N L F E A L N N K N 16 120 L R A K P K V Y I IQ A C R G 16 126 V Y I I Q A C R G E Q R D P G 16 132 C R G E Q R D P GE T V G G D 16 165 A L H V Y S T V E G Y I A Y R 16 169 Y S T V E G Y IA Y R H D Q K 16 185 S C F I Q T L V D V F T K R K 16 191 L V D V F T KR K G H I L E L 16 207 T E V T R R M A E A E L V Q E 16 213 M A E A E LV Q E G K A R K T 16 214 A E A E L V Q E G K A R K T N 16 16 G A R L A LI L C V T K A R E 15 49 E S T M K R D P T A E Q F Q E 15 97 G E D G E MV K L E N L F E A 15 144 G G D E I V M V I K D S P Q T 15 177 A Y R H DQ K G S C F I Q T L 15 226 K T N P E I Q S T L R K R L Y 15 19 L A L I LC V T K A R E G S E 14 36 L D A L E H M F R Q L R F E S 14 54 R D P T AE Q F Q E E L E K F 14 72 I D S R E D P V S C A F V V L 14 73 D S R E DP V S C A F V V L M 14 146 D E I V M V I K D S P Q T I P 14 155 S P Q TI P T Y T D A L H V Y 14 163 T D A L H V Y S T V E G Y I A 14 66 E K F QQ A I D S R E D P V S 13 154 D S P Q T I P T Y T D A L H V 13 162 Y T DA L H V Y S T V E G Y T 13 182 Q K G S C F I Q T L V D V F T 13 225 R KT N P E I Q S T L R K R L 13 1 M S N P R S L E E E K Y D M S 12 6 S L EE E K Y D M S G A R L A 12 153 K D S P Q T I P T Y T D A L H 12 175 Y TA Y R H D Q K G S C F I Q 12 194 V F T K R K G H I L E L L T E 12 197 KR K G H I L E L L T E V T R 12 14 M S G A R L A L I L C V T K A 11 21 LI L C V T K A R E G S E E D 11 22 I L C V T K A R E G S E E D L 11 58 AE Q F Q E E L E K F Q Q A I 11 67 K F Q Q A I D S R E D P V S C 11 103 VK L E N L F E A L N N K N C 11 174 G Y I A Y R H D Q K G S C F I 11 218L V Q E G K A R K T N P E I Q 11 23 L C V T K A R E G S E E D L D 10 25V T K A R E G S E E D L D A L 10 47 R F E S T M K R D P T A E Q F 10 57T A E Q F Q E E L E K F Q Q A 10 62 Q E E L E K F Q Q A I D S R E 10 65L E K F Q Q A I D S R E D P V 10 71 A I D S R E D P V S C A F V V 10 94F L K G E D G E M V K L E N L 10 115 K N C Q A L R A K P K V Y I I 10118 Q A L R A K P K V Y I I Q A C 10 128 I I Q A C R G E Q R D P G E T10 138 D P G E T V G G D E I V M V I 10 143 V G G D E I V M V I K D S PQ 10 172 V E G Y I A Y R H D Q K G S C 10 189 Q T L V D V F T K R K G HI L 10 198 R K G H I L E L L T E V T R R 10 212 R M A E A E L V Q E G KA R K 10 215 E A E L V Q E G K A R K T N P 10 221 E G K A R K T N P E IQ S T L 10 3 N P R S L E E E K Y D M S G A 9 27 K A R E G S E E D L D AL E H 9 31 G S E E D L D A L E H M F R Q 9 35 D L D A L E H M F R Q L RF E 9 37 D A L E H M F R Q L R F E S T 9 41 H M F R Q L R F E S T M K RD 9 48 F E S T M K R D P T A E Q F Q 9 59 E Q F Q E E L E K F Q Q A I D9 60 Q F Q E E L E K F Q Q A I D S 9 75 R E D P V S C A F V V L M A H 985 V L M A H G R E G F L K G E D 9 105 L E N L F E A L N N K N C Q A 9113 N N K N C Q A L R A K P K V Y 9 134 G E Q R D P G E T V G G D E I 9139 P G E T V G G D E I V M V I K 9 161 T Y T D A L H V Y S T V E G Y 9173 E G Y I A Y R H D Q K G S C F 9 181 D Q K G S C F I Q T L V D F 9195 F T K R K G H I L E L L T E V 9 205 L L T E V T R R M A E A E L V 9210 T R R M A E A E L V Q E G K A 9 222 G K A R K T N P E I Q S T L R 9224 A R K T N P E I Q S T L R K R 9 10 E K Y D M S G A R L A L I L C 813 D M S G A R L A L I L C V T K 8 15 S G A R L A L I L C V T K A R 8 28A R E G S E E D L D A L E H M 8 32 S E E D L D A L E H M F R Q L 8 42 MF R Q L R F E S T M K R D P 8 56 P T A E Q F Q E E L E K F Q Q 8 61 F QE E L E K F Q Q A I D S R 8 68 F Q Q A I D S R E D P V S C A 8 77 D P VS C A F V V L M A H G R 8 98 E D G E M V K L E N L F E A L 8 101 E M V KL E N L F E A L N N K 8 108 L F E A L N N K N C Q A L R A 8 112 L N N KN C Q A L R A K P K V 8 125 K V Y I I Q A C R G E Q R D P 8 130 Q A C RG E Q R D P G E T V G 8 136 Q R D P G E T V G G D E I V M 8 141 E T V GG D E I V M V I K D S 8 156 P Q T I P T Y T D A L H V Y S 8 160 P T Y TD A L H V Y S T V E G 8 180 H D Q K G S C F I Q T L V D V 8 186 C F I QT L V D V F T K R K G 8 220 Q E G K A R K T N P E I Q S T 8 7 L E E E KY D M S G A R L A L 7 24 C V T K A R E G S E E D L D A 7 78 P V S C A FV V L M A H G R E 7 116 N C Q A L R A K P K V Y I I Q 7 122 A K P K V YT I Q A C R G E Q 7 152 I K D S P Q T I L P T Y T D A L 7 170 S T V E GY I A Y R H D Q K G 7 219 V Q E G K A R K T N P E I Q S 7 46 L R F E S TM K R D P T A E Q 6 64 E L E K F Q Q A I D S R E D P 6 70 Q A I D S R ED P V S C A F V 6 79 V S C A F V V L M A H G R E G 6 96 K G E D G E M VK L E N L F E 6 131 A C R G E Q R D P G E T V G G 6 142 T V G G D E I VM V I K D S P 6 150 M V I K D S P Q T I P T Y T D 6 151 V I K D S P Q TI P T Y T D A 6 196 T K R K G H I L E L L T E V T 6 87 M A H G R E G F LK G E D G E 5 190 T L V D V F T K R K G H I L E 5 90 G R E G F L K G E DG E M V K 4 133 R G E Q R D P G E T V G G D E 4 2 S N P R S L E E E K YD M S G 3 110 E A L N N K N C Q A L R A K P 3 164 D A L H V Y S T V E GY lA Y 3 171 T V E G Y I A Y R H D Q K G S 3 201 H I L E L L T E V T R RM A E 3 38 A L E H M F R Q L R F E S T M 2 86 L M A H G R E G F L K G ED G 2 129 I Q A C R G E Q R D P G E T V 2 135 E Q R D P G E T V G G D ET V 2 167 H V Y S T V E G Y I A Y R H D 2 178 Y R H D Q K G S C F I Q TL V 2 187 F I Q T L V D V F T K R K G H 2 193 D V F T K R K G H I L E LL T 2 223 I C A R K T N P E I Q S T L R K 2 227 T N P E I Q S T L R K RL Y L 2 26 T K A R E G S E E D L D A L E 1 34 E D L D A L E H M F R Q LR F 1 44 R Q L R F E S T M K R D P T A 1 52 H K R D P T A E Q F Q E E LE 1 53 K R D P T A E Q F Q E E L E K 1 93 G F L K G E D G E M V K L E M1 95 L K G E D G E M V K L E N L F 1 104 K L E N L F E A L N N K N C Q 1107 N L F E A L N N K N C Q A L R 1 119 A L R A K P K V Y I I Q A C R 1121 R A K P K V Y I I Q A C R G E 1 127 Y I I Q A C R G E Q R D P G E 1168 V Y S T V E G Y I A Y R H D Q 1 179 R H D Q K G S C F I Q T L V D 1217 E L V Q E G K A R K T N P E I 1 213P1F11 v.1: HLA-DRB1*0301 (DR17)15-mers 228 N P E I Q S T L R K R L Y L Q 26 83 F V V L M A H G R E G FL K G 25 84 V V L M A H G R E G F L K G E 24 49 E S T M K R D P T A E QF Q E 23 148 I V M V I L K D S P Q T I P T Y 23 140 G E T V G G D E I VM V I K D 22 105 L E N L F E A L N N K C Q A 20 109 F E A L N N K N C QA L R A K 20 19 L A L I L C V T K A R E G S E 19 99 D G E M V K L E N LF E A L N 19 117 C Q A L R A K P K V Y I I Q A 19 215 E A E L V Q E G KA R K T P 19 1 M S N P R S L E E E K Y D M S 18 36 L D A L E H M F R Q LR F E S 18 93 G F L K G E D G E M V K L E N 18 102 M V K L E N L F E A LN N K N 18 145 G D E I V M V I K D S P Q T I 18 149 V M V I K D S P Q TI P T Y T 18 158 T I P T Y T D A L H V Y S T V 18 184 G S C F I Q T L VD V F T K R 18 192 V D V F T K R K G H I L E L L 18 200 G H I L E L L TE V T R R M A 18 203 L E L L T E V T R R M A E A E 18 10 E K Y D M S G AR L A L T L C 17 22 I L C V T K A R E G S E E D L 17 25 V T K A R E G SE E D L D A L 17 32 S E E D L D A L E H M F R Q L 17 39 L E H M F R Q LR F E S T M K 17 62 Q E E L E K F Q Q A I D S R E 17 67 K F Q Q A I D SR E D P V S C 17 98 E D G E M V K L E N L F E A L 17 125 K V Y I I Q A CR G E Q R D P 17 165 A L H V Y S T V E G Y I A Y R 17 175 Y I A Y R H DQ K G S C F I Q 17 189 Q T L V D V F T K R K G H I L 17 37 D A L E H M FR Q L R F E S T 16 58 A E Q F Q E E L E K F Q Q A I 16 191 L V D V F T KR K G H I L E L 16 207 T E V T R R M A E A E L V Q E 16 45 Q L R F E S TM K R D P T A E 15 54 R D P T A E Q F Q E E L E K F 15 106 E N L F E A LN N K N C Q A L 15 224 A R K T N P E I Q S T L R K R 15 29 R E G S E E DL D A L E H M F 14 199 K G H I L E L L T E V T R R M 14 16 G A R L A L TL C V T K A R E 13 18 R L A L I L C V T K A R E G S 13 43 F R Q L R F ES T M K R D P T 13 71 A T D S R E D P V S C A F V V 13 82 A F V V L M AH G R E G F L K 13 101 E M V K L E N L F E A L N N K 13 187 F I Q T L VD V F T K R K G H 13 210 T R R M A E A E L V Q E G K A 13 216 A E L V QE G K A R K T N P E 13 4 P R S L E E E K Y D M S G A R 12 7 L E E E K YD M S G A R L A L 12 11 K Y D M S G A R L A L I L C V 12 69 Q Q A I D SR E D P V S C A F 12 76 E D P V S C A F V V L M A H G 12 81 C A F V V LM A H G R E G F L 12 100 G E M V K L E N L F E A L N N 12 156 P Q T I PT Y T D A L H V Y S 12 163 T D A L H V Y S T V E G Y T A 12 173 E G Y IA Y R H D Q K G S C F 12 202 I L E L L T E V T R R M A E A 12 206 L T EV T R R M A E A E L V Q 12 20 A L I L C V T K A R E G S E E 11 31 G S EE D L D A L E H M F R Q 11 33 E E D L D A L E H M F R Q L R 11 35 D L DA L E H M F R Q L R F E 11 61 F Q E E L E K F Q Q A I D S R 11 75 R E DP V S C A F V V L M A H 11 91 R E G F L K G E D G E M V K L 11 92 E G FL K G E D G E M V K L E 11 94 F L K G E D G E M V K L E N L 11 97 G E DG E M V K L E N L F E A 11 116 N C Q A L R A K P K V Y I I Q 11 132 C RG E Q R D P G E T V G G D 11 146 D E I V M V I K D S P Q T I P 11 147 ET V M V I K D S P Q T I P T 11 155 S P Q T I P T Y T D A L H V Y 11 167H V Y S T V E G Y I A Y R H D 11 185 S C F I Q T L V D V F T K R K 11188 I Q T L V D V F T K R K G H I 11 3 N P R S L E E E K Y D M S G A 108 E E E K Y D M S G A R L A L I 10 12 Y D M S G A R L A L I L C V T 1028 A R E G S E E D L D A L E H M 10 57 T A E Q F Q E E L E K F Q Q A 10123 K P K V Y I I Q A C R G E Q R 10 126 V Y I I Q A C R G E Q R D P G10 169 Y S T V E G Y I A Y R H D Q K 10 180 H D Q K G S C F I Q T L V DV 10 194 V F T K R K G H I L E L L T E 10 195 F T K R K G H I L E L L TE V 10 40 E H M F R Q L R F E S T M K R 9 50 S T M K R D P T A E Q F Q EE 9 72 I D S R E D P V S C A F V V L 9 80 S C A F V V L M A H G R E G F9 108 L F E A L N N K N C Q A L R A 9 113 N N K N C Q A L R A K P K V Y9 151 V I K D S P Q T I P T Y T D A 9 164 D A L H V Y S T V E G Y lA Y 9176 I A Y R H D Q K G S C F I Q T 9 196 T K R K G I I I L E L L T E V T9 2 S N P R S L E E E K Y D M S G 8 26 T K A R E G S E E D L D A L E 851 T M K R D P T A E Q F Q E E L 8 56 P T A E Q F Q E E L E K F Q Q 8 59E Q F Q E E L E K F Q Q A I D 8 65 L E K F Q Q A I D S R E D P V 8 90 GR E G F L K G E D G E M V K 8 96 K G E D G E M V K L E N L F E 8 107 N LF E A L N N K N C Q A L R 8 110 E A L N N K N C Q A L R A K P 8 115 K NC Q A L R A K P K V Y I I 8 122 A K P K V Y I I Q A C R G E Q 8 127 Y II Q A C R G E Q R D P G E 8 133 R G E Q R D P G E T V G G D E 8 190 T LV D V F T K R K G H I L E 8 213 M A E A E L V Q E G K A R K T 8 222 G KA R K T N P E I Q S T L R 8 21 L I L C V T K A R E G S E E D 7 41 H M FR Q L R F E S T M K R D 7 46 L R F E S T M K R D P T A E Q 7 52 M K R DP T A E Q F Q E E L E 7 55 D P T A E Q F Q E E L E K F Q 7 68 F Q Q A ID S R E D P V S C A 7 88 A H G R E G F L K G E D G E M 7 128 I I Q A C RG E Q R D P G E T 7 129 I Q A C R G E Q R D P G E T V 7 139 P G E T V GG D E I V M V T K 7 181 D Q K G S C F I Q T L V D V F 7 204 E L L T E VT R R M A E A E L 7 209 V T R R M A E A E L V Q E G K 7 212 R M A E A EL V Q E G K A R K 7 218 L V Q E G K A R K T N P E I Q 7 171 T V E G Y IA Y R H D Q K G S 6 174 G Y I A Y R H D Q K G S C F I 6 217 E L V Q E GK A R K T N P E I 6 220 Q E G K A R K T N P E I Q S T 6 14 M S G A R L AL I L C V T K A 4 103 V K L E N L F E A L N N K N C 4 104 K L E N L F EA L N N K N C Q 4 201 H I L E L L T E V T R R M A E 4 208 E V T R R H AE A E L V Q E G 4 214 A E A E L V Q E G K A R K T N 4 9 E E K Y D M S GA R L A L I L 3 17 A R L A L I L C V T K A R E G 3 27 K A R E G S E E DL D A L E H 3 42 M F R Q L R F E S T M K R D P 3 60 Q F Q E E L E K F QQ A I D S 3 73 D S R E D P V S C A F V V L M 3 86 L M A H G R E G F L KG E D G 3 121 R A K P K V Y I I Q A C R G E 3 134 G E Q R D P G E T V GG D E I 3 159 I P T Y T D A L H V Y S T V E 3 168 V Y S T V E G Y I A YR H D Q 3 193 D V F T K R K G H T L E L L T 3 198 R K G H I L E L L T EV T R R 3 219 V Q E G K A R K T N P E I Q S 3 223 K A R K T N P E I Q ST L R K 3 15 S G A R L A L I L C V T K A R 2 23 L C V T K A R E G S E ED L D 2 47 R F E S T M K R D P T A E Q F 2 53 K R D P T A E Q F Q E E LE K 2 79 V S C A F V V L M A H G R E G 2 85 V L M A H G R E G F L K G ED 2 87 M A H G R E G F L K G E D G E 2 111 A L N N K N C Q A L R A K P K2 119 A L R A K P K V Y I I Q A C R 2 138 D P G E T V G G D E I V M V I2 142 T V G G D E T V M V I K D S P 2 157 Q T I P T Y T D A L H V Y S T2 162 Y T D A L H V Y S T V E G Y I 2 186 C F T Q T L V D V F T K R K G2 197 K R K G H I L E L L T E V T R 2 205 L L T E V T R R M A E A E L V2 211 R R M A E A E L V Q E G K A R 2 225 R K T N P E I Q S T L R K R L2 226 K T N P E I Q S T L R K R L Y 2 227 T N P E I Q S T L R K R L Y L2 5 R S L E E E K Y D M S G A R L 1 13 D M S G A R L A L I L C V T K 124 C V T K A R E G S E E D L D A 1 30 E G S E E D L D A L E H M F R 1 34E D L D A L E H M F R Q L R F 1 44 R Q L R F E S T M K R D P T A 1 48 FE S T M K R D P T A E Q F Q 1 63 E E L E K F Q Q A I D S R E D 1 70 Q AT D S R E D P V S C A F V 1 77 D P V S C A F V V L M A H G R 1 78 P V SC A F V V L M A H G R E 1 89 H G R E G F L K G E D G E M V 1 95 L K G ED G E M V K L E N L F 1 112 L N N K N C Q A L R A K P K V 1 118 Q A L RA K P K V Y I I Q A C 1 124 P K V Y I I Q A C R G E Q R D I 130 Q A C RG E Q R D P G E T V G I 136 Q R D P G E T V G G D E I V M 1 137 R D P GE T V G G D E I V M V 1 143 V G G D E I V M V I K D S P Q 1 144 G G D EI V M V I K D S P Q T 1 150 M V T K D S P Q T I P T Y T D 1 153 K D S PQ T I P T Y T D A L H 1 154 D S P Q T I P T Y T D A L H V 1 161 T Y T DA L H V Y S T V E G Y 1 166 L H V Y S T V E G Y I A Y R H 1 172 V E G YI A Y R H D Q K G S C 1 177 A Y R H D Q K G S C F I Q T L I 178 Y R H DQ K G S C F I Q T L V 1 179 R H D Q K G S C F I Q T L V D 1 182 Q K G SC F I Q T L V D V F T 1 183 K G S C F I Q T L V D V F T K I 221 E G K AR K T N P E I Q S T L 1 213P1F11 v.1:HLA-DRB1*0401 (DR4Dw4) 15-mers 159I P T Y T D A L H V Y S T V E 28 49 E S T H K R D P T A E Q F Q E 26 105L E N L F E A L N N K N C Q A 26 125 K V Y I I Q A C R G E Q R D P 26188 I Q T L V D V F T K R K G H I 26 199 K G H I L E L L T E V T R R M26 202 I L E L L T E V T R R M A E A 26 203 L E L L T E V T R R M A E AE 26 40 E H M F R Q L R F E S T M K R 22 58 A E Q F Q E E L E K F Q Q AI 22 106 E N L F E A L N N K N C Q A L 22 166 L H V Y S T V E G Y I A YR H 22 172 V E G Y I A Y R H D Q K G S C 22 4 P R S L E E E K Y D M S GA R 20 11 K Y D H S G A R L A L I L C V 20 16 G A R L A L I L C V T K AR E 20 33 E E D L D A L E H M F R Q L R 20 39 L E H N F R Q L R F E S TM K 20 43 F R Q L R F E S T M K R D P T 20 62 Q E E L E K F Q Q A T D SR E 20 76 E D P V S C A F V V L M A H G 20 92 E G F L K G E D G E M V KL E 20 99 D G E M V K L E N L F E A L N 20 100 G E M V K L E N L F E A LN N 20 102 M V K L E N L F E A L N N K N 20 140 G E T V G G D E I V M VI K D 20 146 D E I V M V I K D S P Q T I P 20 148 I V M V I K D S P Q TI P T Y 20 185 S C F I Q T L V D V F T K R K 20 215 E A E L V Q E G K AR K T N P 20 228 N P E I Q S T L R K R L Y L Q 20 42 M F R Q L R F E S TM K R D P 18 171 T V E G Y I A Y R H D Q K G S 18 181 D Q K G S C F I QT L V D V F 18 212 R M A E A E L V Q E G K A R K 18 224 A R K T N P E IQ S T L R K R 18 9 E E K Y D M S G A R L A L I L 16 65 L E K F Q Q A I DS R E D P V 16 80 S C A F V V L M A H G R E G F 16 91 R E G F L K G E DG E M V K L 16 175 Y I A Y R H D Q K G S C F I Q 16 147 E T V M V I K DS P Q T I P T 15 18 R L A L I L C V T K A R E G S 14 19 L A L I L C V TK A R E G S E 14 22 I L C V T K A R E G S E E D L 14 36 L D A L E H M FR Q L R F E S 14 81 C A F V V L H A H G R E G F L 14 82 A F V V L M A HG R E G F L K 14 83 F V V L M A H G R E G F L K G 14 84 V V L M A H G RE G F L K G E 14 123 K P K V Y I I Q A C R G E Q R 14 145 G D E I V M VI K D S P Q T I 14 149 V M V I K D S P Q T I P T Y T 14 163 T D A L H VY S T V E G Y I A 14 165 A L H V Y S T V E G Y I A Y R 14 189 Q T L V DV F T K R K G H I L 14 200 G H I L E L L T E V T R R M A 14 210 T R R HA E A E L V Q E G K A 14 216 A E L V Q E G K A R K T N P E 14 3 N P R SL E E E K Y D M S G A 12 7 L E E E K Y D M S G A R L A L 12 10 E K Y D MS G A R L A L I L C 12 14 M S G A R L A L I L C V T K A 12 15 S G A R LA L I L C V T K A R 12 17 A R L A L I L C V T K A R E G 12 24 C V T K AR E G S E E D L D A 12 27 K A R E G S E E D L D A L E H 12 28 A R E G SE E D L D A L E H M 12 31 G S E E D L D A L E H M F R Q 12 34 E D L D AL E H M F R Q L R F 12 37 D A L E H M F R Q L R F E S T 12 46 L R F E ST M K R D P T A E Q 12 52 M K R D P T A E Q F Q E E L E 12 54 R D P T AE Q F Q E E L E K F 12 59 E Q F Q E E L E K F Q Q A I D 12 60 Q F Q E EL E K F Q Q A I D S 12 66 E K F Q Q A I D S R E D P V S 12 67 K F Q Q AI D S R E D P V S C 12 71 A I D S R E D P V S C A F V V 12 73 D S R E DP V S C A F V V L M 12 77 D P V S C A F V V L M A H G R 12 93 G F L K GE D G E M V K L E N 12 97 G E D G E M V K L E N L F E A 12 103 V K L E NL F E A L N N K N C 12 104 K L E N L F E A L N N K N C Q 12 108 L F E AL N N K N C Q A L R A 12 113 N N K N C Q A L R A K P K V Y 12 114 N K NC Q A L R A K P K V Y T 12 120 L R A K P K V Y I I Q A C R G 12 122 A KP K V Y I I Q A C R G E Q 12 129 I Q A C R G E Q R D P G E T V 12 132 CR G E Q R D P G E T V G G D 12 137 R D P G E T V G G D E I V M V 12 141E T V G G D E I V M V I K D S 12 142 T V G G D E I V M V I K D S P 12150 M V I K D S P Q T I P T Y T D 12 153 K D S P Q T I P T Y T D A L H12 155 S P Q T I P T Y T D A L H V Y 12 160 P T Y T D A L H V Y S T V EG 12 162 Y T D A L H V Y S T V E G Y I 12 174 G Y I A Y R H D Q K G S CF I 12 182 Q K G S C F I Q T L V D V F T 12 186 C F I Q T L V D V F T KR K G 12 196 T K R K G H I L E L L T E V T 12 198 R K G H I L E L L T EV T R R 12 208 E V T R R M A E A E L V Q E G 12 209 V T R R M A E A E LV Q E G K 12 213 H A E A E L V Q E G K A R K T 12 225 R K T N P E I Q ST L R K R L 12 226 K T N P E I Q S T L R K R L Y 12 192 V D V F T K R KG H I L E L L 11 45 Q L R F E S T M K R D P T A E 10 124 P K V Y I I Q AC R G E Q R D 10 184 G S C F I Q T L V D V F T K R 10 69 Q Q A I D S R ED P V S C A F 9 109 F E A L N N K N C Q A L R A K 9 117 C Q A L R A K PK V Y T I Q A 9 191 L V D V F T K R K G H I L E L 9 20 A L I L C V T K AR E G S E E 8 126 V Y I I Q A C R G E Q R D P G 8 156 P Q T I P T Y T DA L H V Y S 8 169 Y S T V E G Y I A Y R H D Q K 8 21 L I L C V T K A R EG S E E D 7 61 F Q E E L E K F Q Q A I D S R 7 177 A Y R H D Q K G S C FI Q T L 7 217 E L V Q E G K A R K T N P E I 7 220 Q E G K A R K T N P EI Q S T 7 1 M S N P R S L E E E K Y D M S 6 2 S N P R S L E E E K Y D MS G 6 6 S L E E E K Y D M S G A R L A 6 8 E E E K Y D M S G A R L A L I6 13 D M S G A R L A L I L C V T K 6 25 V T K A R E G S E E D L D A L 629 R E G S E E D L D A L E H M F 6 30 E G S E E D L D A L E H M F R 6 32S E E D L D A L E H M F R Q L 6 35 D L D A L E H M F R Q L R F E 6 51 TM K R D P T A E Q F Q E E L 6 53 K R D P T A E Q F Q E E L E K 6 55 D PT A E Q F Q E E L E K F Q 6 56 P T A E Q F Q E E L E K F Q Q 6 57 T A EQ F Q E E L E K F Q Q A 6 63 E E L E K F Q Q A I D S R E D 6 68 F Q Q AI D S R E D P V S C A 6 70 Q A I D S R E D P V S C A F V 6 72 I D S R ED P V S C A F V V L 6 74 S R E D P V S C A F V V L M A 6 75 R E D P V SC A F V V L M A H 6 78 P V S C A F V V L M A H G R E 6 79 V S C A F V VL M A H G R E G 6 86 L M A H G R E G F L K G E D G 6 88 A H G R E G F LK G E D G E M 6 89 H G R E G F L K G E D G E M V 6 94 F L K G E D G E HV K L E N L 6 95 L K G E D G E M V K L E N L F 6 96 K G E D G E M V K LE N L F E 6 101 E M V K L E N L F E A L N N K 6 107 N L F E A L N N K NC Q A L R 6 110 E A L N N K N C Q A L R A K P 6 111 A L N N K N C Q A LR A K P K 6 112 L N N K N C Q A L R A K P K V 6 116 N C Q A L R A K P KV Y I I Q 6 118 Q A L R A K P K V Y I I Q A C 6 128 I I Q A C R G E Q RD P G E T 6 134 G E Q R D P G E T V G G D E I 6 135 E Q R D P G E T V GG D E I V 6 138 D P G E T V G G D E I V M V I 6 139 P G E T V G G D E IV M V I K 6 143 V G G D E I V M V I K D S P Q 6 144 G G D E I V M V I KD S P Q T 6 152 I K D S P Q T I P T Y T D A L 6 154 D S P Q T I P T Y TD A L H V 6 157 Q T I P T Y T D A L H V Y S T 6 158 T I P T Y T D A L HV Y S T V 6 161 T Y T D A L H V Y S T V E G Y 6 167 H V Y S T V E G Y IA Y R H D 6 170 S T V E G Y I A Y R H D Q K G 6 178 Y R H D Q K G S C FI Q T L V 6 179 R H D Q K G S C F I Q T L V D 6 180 H D Q K G S C F I QT L V D V 6 183 K G S C F I Q T L V D V F T K 6 187 F I Q T L V D V F TK R K G H 6 190 T L V D V F T K R K G H I L E 6 194 V F T K R K G H I LE L L T E 6 195 F T K R K G H I L E L L T E V 6 197 K R K G H I L E L LT E V T R 6 204 E L L T E V T R R M A E A E L 6 207 T E V T R R M A E AE L V Q E 6 211 R R M A E A E L V Q E G K A R 6 218 L V Q E G K A R K TN P E I Q 6 221 E G K A R K T N P E I Q S T L 6 222 G K A R K T N P E TQ S T L R 6 223 K A R K T N P E I Q S T L R K 6 173 E G Y I A Y R H D QK G S C F 3 206 L T E V T R R M A E A E L V Q 3 12 Y D M S G A R L A L IL C V T 1 41 H M F R Q L R F E S T M K R D 1 47 R F E S T M K R D P T AE Q F 1 85 V L M A H G R E G F L K G E D 1 115 K N C Q A L R A K P K V YI I I 119 A L R A K P K V Y I I Q A C R 1 131 A C R G E Q R D P G E T VG G 1 193 D V F T K R K G H I L E L L T 1 205 L L T E V T R R M A E A EL V 1 219 V Q E G K A R K T N P E I Q S 1 5 R S L E E E K Y D M S G A RL -5 23 L C V T K A R E G S E E D L D -5 38 A L E H M F R Q L R F E S TM -5 48 F E S T M K R D P T A E Q F Q -5 90 G R E G F L K G E D G E M VK -5 98 E D G E M V K L E N L F E A L -5 127 Y I I Q A C R G E Q R D P GE -5 213P1F11 v.1: HLA-DRB1*1101 15-mers 203 L E L L T E V T R R M A E AE 29 145 G D E I V M V I K D S P Q T I 26 159 I P T Y T D A L H V Y S TV E 26 45 Q L R F E S T M K R D P T A E 25 166 L H V Y S T V E G Y I A YR H 23 189 Q T L V D V F T K R K G H I L 23 19 L A L I L C V T K A R E GS E 22 81 C A F V V L M A H G R E G F L 22 36 L D A L E H M F R Q L R FE S 21 39 L E H M F R Q L R F E S T M K 21 33 E E D L D A L E I I M F RQ L R 20 123 K P K V Y I I Q A C R G E Q R 20 9 E E K Y D M S G A R L AL T L 18 172 V E G Y I A Y R H D Q K G S C 18 175 Y I A Y R H D Q K G SC F I Q 18 80 S C A F V V L M A I I G R E G F 17 40 E H M F R Q L R F ES T M K R 16 96 K G E D G E M V K L E N L F E 16 106 E N L F E A L N N KN C Q A L 16 215 E A E L V Q E G K A R K T N P 16 228 N P E I Q S T L RK R L Y L Q 16 113 N N K N C Q A L R A K P K V Y 15 144 G G D E I V M VI K D S P Q T 15 191 L V D V F T K R K G H I L E L 15 20 A L I L C V T KA R E G S E E 14 21 L I L C V T K A R E G S E E D 14 46 L R F E S T M KR D P T A E Q 14 59 E Q F Q E E L E K F Q Q A I D 14 67 K F Q Q A I D SR E D P V S C 14 79 V S C A F V V L M A H G R E G 14 83 F V V L M A H GR E G F L K G 14 117 C Q A L R A K P K V Y I I Q A 14 125 K V Y I I Q AC R G E Q R D P 14 129 I Q A C R G E Q R D P G E T V 14 185 S C F I Q TL V D V F T K R K 14 188 I Q T L V D V F T K R K G H I 14 218 L V Q E GK A R K T N P E I Q 14 17 A R L A L I L C V T K A R E G 13 69 Q Q A I DS R E D P V S C A F 13 82 A F V V L M A H G R E G F L K 13 102 H V K L EN L F E A L N N K N i3 146 D E I V M V I K D S P Q T I P 13 149 V M V IK D S P Q T I P T Y T 13 163 T D A L H V Y S T V E G Y I A 13 173 E G YI A Y R H D Q K G S C F 13 192 V D V F T K R K G H I L E L L 13 199 K GH I L E L L T E V T R R M 13 213 M A E A E L V Q E G K A R K T 13 4 P RS L E E E K Y D M S G A R 12 16 G A R L A L I L C V T K A R E 12 65 L EK F Q Q A I D S R E D P V 12 89 H G R E G F L K G E D G E M V 12 99 D GE M V K L E N L F E A L N 12 100 G E M V K L E N L F E A L N N 12 120 LR A K P K V Y I I Q A C R G 12 200 G H I L E L L T E V T R R M A 12 124P K V Y I I Q A C R G E Q R D 11 184 G S C F I Q T L V D V F T K R 11202 I L E L L T E V T R R M A E A 11 58 A E Q F Q E E L E K F Q Q A I 1091 R E G F L K G E D G E M V K L 10 115 K N C Q A L R A K P K V Y I I 9142 T V G G D E I V M V I K D S P 9 193 D V F T K R K G H I L E L L T 9204 E L L T E V T R R M A E A E L 9 3 N P R S L E E E I C Y D M S G A 88 E E E K Y D M S G A R L A L I 8 10 E K Y D M S G A R L A L I L C 8 18R L A L I L C V T K A R E G S 8 22 I L C V T K A R E G S E E D L 8 47 RF E S T M K R D P T A E Q F 8 77 D P V S C A F V V L M A H G R 8 78 P VS C A F V V L M A H G R E 8 88 A H G R E G F L K G E D G E M 8 105 L E NL F E A L N N K N C Q A 8 107 N L F E A L N N K N C Q A L R 8 111 A L NN K N C Q A L R A K P K 8 154 D S P Q T I P T Y T D A L H V 8 165 A L HV Y S T V E G Y I A Y R 8 169 Y S T V E G Y I A Y R H D Q K 8 171 T V EG Y I A Y R H D Q K G S 8 186 C F I Q T L V D V F T K R K G 8 190 T L VD V F T K R K G H I L E 8 206 L T E V T R R M A E A E L V Q 8 212 R M AE A E L V Q E G K A R K 8 216 A E L V Q E G K A R K T N P E 8 217 E L VQ E G K A R K T N P E I 8 1 M S N P R S L E E E K Y D M S 7 11 K Y D M SG A R L A L I L C V 7 13 D M S G A R L A L I L C V T K 7 15 S G A R L AL I L C V T K A R 7 43 F R Q L R F E S T M K R D P T 7 62 Q E E L E K FQ Q A I D S R E 7 66 E K F Q Q A I D S R E D P V S 7 76 E D P V S C A FV V L M A H G 7 86 L M A H G R E G F L K G E D G 7 128 I I Q A C R G E QR D P G E T 7 133 R G E Q R D P G E T V G G D E 7 143 V G G D E I V M VI K D S P Q 7 156 P Q T I P T Y T D A L H V Y S 7 162 Y T D A L H V Y ST V E G Y I 7 170 S T V E G Y I A Y R H D Q K G 7 182 Q K G S C F I Q TL V D V F T 7 196 T K R K G H I L E L L T E V T 7 225 R K T N P E I Q ST L R K R L 7 5 R S L E E E K Y D M S G A R L 6 6 S L E E E K Y D M S GA R L A 6 27 K A R E G S E E D L D A L E H 6 30 E G S E E D L D A L E HM F R 6 49 E S T M K R D P T A E Q F Q E 6 60 Q F Q E E L E K F Q Q A ID S 6 63 E E L E K F Q Q A I D S R E D 6 71 A I D S R E D P V S C A F VV 6 73 D S R E D P V S C A F V V L M 6 84 V V L M A H G R E G F L K G E6 92 E G F L K G E D G E M V K L E 6 97 G E D G E M V K L E N L F E A 6108 L F E A L N N K N C Q A L R A 6 109 F E A L N N K N C Q A L R A K 6114 N K N C Q A L R A K P K V Y I 6 122 A K P K V Y I I Q A C R G E Q 6126 V Y I I Q A C R G E Q R D P G 6 134 G E Q R D P G E T V G G D E I 6137 R D P G E T V G G D E I V M V 6 140 G E T V G G D E I V M V I K D 6147 E I V M V I K D S P Q T I P T 6 148 I V M V I K D S P Q T I P T Y 6153 K D S P Q T I P T Y T D A L H 6 160 P T Y T D A L H V Y S T V E G 6174 G Y I A Y R H D Q K G S C F I 6 197 K R K G H I L E L L T E V T R 6205 L L T E V T R R M A E A E L V 6 207 T E V T R R M A E A E L V Q E 6210 T R R M A E A E L V Q E G K A 6 211 R R M A E A E L V Q E G K A R 6222 G K A R K T N P E I Q S T L R 6 138 D P G E T V G G D E I V M V I 4187 F I Q T L V D V F T K R K G H 4 44 R Q L R F E S T M K R D P T A 3119 A L R A K P K V Y I T Q A C R 3 167 H V Y S T V E G Y I A Y R H D 334 E D L D A L E H M F R Q L R F 2 37 D A L E H M F R Q L R F E S T 2 53K R D P T A E Q F Q E E L E K 2 57 T A E Q F Q E E L E K F Q Q A 2 72 ID S R E D P V S C A F V V L 2 74 S R E D P V S C A F V V L M A 2 98 E DG E M V K L E N L F E A L 2 127 Y I I Q A C R G E Q R D P G E 2 136 Q RD P G E T V G G D E I V M 2 157 Q T I P T Y T D A L H V Y S T 2 161 T YT D A L H V Y S T V E G Y 2 201 H I L E L L T E V T R R M A E 2 223 K AR K T N P E I Q S T L R K 2 226 K T N P E I Q S T L R K R L Y 2 227 T NP E I Q S T L R K R L Y L 2 12 Y D M S G A R L A L I L C V T 1 26 T K AR E G S E E D L D A L E 1 29 R E G S E E D L D A L E H M F 1 35 D L D AL E H M F R Q L R F E 1 38 A L E H M F R Q L R F E S T M 1 55 D P T A EQ F Q E E L E K F Q 1 64 E L E K F Q Q A I D S R E D P 1 75 R E D P V SC A F V V L M A H 1 85 V L M A H G R E G F L K G E D 1 90 G R E G F L KG E D G E M V K 1 93 G F L K G E D G E M V K L E N 1 94 F L K G E D C EM V K L E N L 1 95 L K G E D G E M V K L E N L F 1 110 E A L N N K N C QA L R A K P 1 112 L N N K N C Q A L R A K P K V 1 116 N C Q A L R A K PK V Y I I Q 1 118 Q A L R A K P K V Y I I Q A C 1 121 R A K P K V Y I IQ A C R G E 1 139 P G E T V G G D E I V M V I K 1 TABLE XIXC, part 2:MHC Class II 15-mer analysis of 213P1F11 v.2 (aa 1-230). 213P1F11 v.2:HLA-DRB1*0101 15-mers 6 L H V Y S T V E G P T P F Q D 33 55 P W W M C SR R G K D I S W N 25 32 P P L W N S Q D T S P T D M I 23 18 F Q D P L YL P S E A P P N P 22 21 P L Y L P S E A P P N P P L W 22 13 E G P T P FQ D P L Y L P S E 21 43 T D M I R K A H A L S R P W W 20 20 D P L Y L PS E A P P N P P L 19 41 S P T D M I R K A H A L S R P 19 15 P T P F Q DP L Y L P S E A P 18 7 H V Y S T V E G P T P F Q D P 17 19 Q D P L Y L PS E A P P N P P 17 31 N P P L W N S Q D T S P T D M 17 42 P T D M I R KA H A L S R P W 16 49 A H A L S R P W W M C S R R G 16 17 P F Q D P L YL P S E A P P N 15 34 L W N S Q D T S P T D M I R K 15 40 T S P T D M IR K A H A L S R 15 47 R K A H A L S R P W W M C S R 15 3 T D A L H V Y ST V E G P T P 14 9 Y S T V E G P T P F Q D P L Y 14 22 L Y L P S E A P PN P P L W N 14 35 W N S Q D T S P T D M I R K A 14 53 S R P W W M C S RR G K D I S 14 2 Y T D A L H V Y S T V E G P T 13 52 L S R P W W M C S RR G K D I 13 4 D A L H V Y S T V E G P T P F 11 54 R P W W M C S R R G KD I S W 11 38 Q D T S P T D M I R K A H A L 10 1 T Y T D A L H V Y S T VE G P 9 44 D M I R K A H A L S R P W W M 9 56 W W M C S R R G K D I S WN F 9 5 A L H V Y S T V E G P T P F Q 8 10 S T V E G P T P F Q D P L Y L8 11 T V E G P T P F Q D P L Y L P 8 14 G P T P F Q D P L Y L P S E A 816 T P F Q D P L Y L P S E A P P 8 23 Y L P S E A P P N P P L wN S 8 26S E A P P N P P L W N S Q D T 8 28 A P P N P P L W N S Q D T S P 8 30 PN P P L W N S Q D T S P T D 8 39 D T S P T D M I R K A H A L S 8 46 I RK A H A L S R P W W M C S 8 8 V Y S T V E G P T P F Q D P L 7 29 P P N PP L W N S Q D T S P T 7 45 M I R K A H A L S R P W W M C 7 24 L P S E AP P N P P L W N S Q 6 25 P S E A P P N P P L W N S Q D 6 33 P L W N S QD T S P T D M I R 6 50 H A L S R P W W M C S R R G K 2 12 V E G P T P FQ D P L Y L P S 1 27 E A P P N P P L W N S Q D T S 1 36 N S Q D T S P TD M I R K A H 1 213P1F11 v.2: HLA-DRB1*0301 (DR17) 15-mers 19 Q D P L YL P S E A P P N P P 19 5 A L H V Y S T V E G P T P F Q 17 23 Y L P S E AP P N P P L W N S 15 11 T V E G P T P F Q D P L Y L P 14 42 P T D H I RK A H A L S R P W 13 3 T D A L H V Y S T V E G P T P 12 14 G P T P F Q DP L Y L P S E A 12 21 P L Y L P S E A P P N P P L W 12 43 T D M I R K AH A L S R P W W 12 12 V E G P T P F Q D P L Y L P S 11 38 Q D T S P T DM I R K A H A L 11 55 P W W M C S R R G K D I S W N 11 7 H V Y S T V E GP T P F Q D P 10 9 Y S T V E G P T P F Q D P L Y 10 15 P T P F Q D P L YL P S E A P 10 31 N P P L W N S Q D T S P T D M 10 33 P L W N S Q D T SP T D M I R 10 41 S P T D M I R K A H A L S R P 10 49 A H A L S R P W WM C S R R G 10 13 E G P T P F Q D P L Y L P S E 9 30 P N P P L W N S Q DT S P T D 9 39 D T S P T D M I R K A H A L S 8 40 T S P T D M I R K A HA L S R 8 53 S R P W W M C S R R G K D I S 8 28 A P P N P P L W N S Q DT S P 7 46 I R K A H A L S R P W W M C S 7 54 R P W W M C S R R G K D IS W 7 56 W W M C S R R G K D I S W N F 7 18 F Q D P L Y L P S E A P P NP 4 20 D P L Y L P S E A P P N P P L 4 48 K A H A L S R P W W M C S R R4 8 V Y S T V E G P T P F Q D P L 3 10 S T V E G P T P F Q D P L Y L 322 L Y L P S E A P P N P P L W N 3 25 P S E A P P N P P L W N S Q D 3 27E A P P N P P L W N S Q D T S 3 2 Y T D A L H V Y S T V E G P T 2 17 P FQ D P L Y L P S E A P P N 2 24 L P S E A P P N P P L W N S Q 2 26 S E AP P N P P L W N S Q D T 2 29 P P N P P L W N S Q D T S P T 2 36 N S Q DT S P T D M I R K A H 2 50 H A L S R P W W M C S R R G K 2 1 T Y T D A LH V Y S T V E G P I 4 D A L H V Y S T V E G P T P F 1 6 L H V Y S T V EG P T P F Q D I 16 T P F Q D P L Y L P S E A P P I 32 P P L W N S Q D TS P T D M I 1 34 L W U S Q D T S P T D M I R K 1 35 W N S Q D T S P T DM I R K A 1 37 S Q D T S P T D M I R K A H A 1 44 D M I R K A H A L S RP W W M 1 45 M I R K A H A L S R P W W M C I 47 R K A H A L S R P W W MC S R 1 213P1F11 v.2: HLA-DRB1*0401 (DR4Dw4) 15-mers 32 P P L W N S Q DT S P T D M I 22 53 S R P W W M C S R R G K D I S 22 6 L H V Y S T V E GP T P F Q D 16 15 P T P F Q D P L Y L P S E A P 16 20 D P L Y L P S E AP P N P P L 16 54 R P W W M C S R R G K D I S W 16 42 P T D M I R K A HA L S R P W 15 3 T D A L H V Y S T V E G P T P 14 5 A L H V Y S T V E GP T P F Q 14 21 P L Y L P S E A P P N P P L W 14 43 T D M I R K A H A LS R P W W 14 49 A H A L S R P W W M C S R R G 14 2 Y T D A L H V Y S T VE G P T 12 8 V Y S T V E G P T P F Q D P L 12 11 T V E G P T P F Q D P LY L P 12 18 F Q D P L Y L P S E A P P N P 12 23 Y L P S E A P P N P P LW N S 12 28 A P P N P P L W N S Q D T S P 12 29 P P N P P L W N S Q D TS P T 12 30 P N P P L W N S Q D T S P T D 12 33 P L W N S Q D T S P T DM T R 12 35 W N S Q D T S P T D M I R K A 12 38 Q D T S P T D M I R K AH A L 12 40 T S P T D M I R K A H A L S R 12 45 M T R K A H A L S R P WW M C 12 46 I R K A H A L S R P W W M C S 12 55 P W W M C S R R G K D IS W N 9 9 Y S T V E G P T P F Q D P L Y 8 19 Q D P L Y L P S E A P P N PP 8 31 N P P L W N S Q D T S P T D M 8 1 T Y T D A L H V Y S T V E G P 67 H V Y S T V E G P T P F Q D P 6 12 V E G P T P F Q D P L Y L P S 6 13E G P T P F Q D P L Y L P S E 6 14 G P T P F Q D P L Y L P S E A 6 16 TP F Q D P L Y L P S E A P P 6 17 P F Q D P L Y L P S E A P P N 6 22 L YL P S E A P P N P P L W N 6 25 P S E A P P N P P L W N S Q D 6 26 S E AP P N P P L W N S Q D T 6 27 E A P P N P P L W N S Q D T S 6 34 L W N SQ D T S P T D M T R K 6 37 S Q D T S P T D M I R K A H A 6 39 D T S P TD H I R K A H A L S 6 47 R K A H A L S R P W W M C S R 6 52 L S R P W WM C S R R G K D I 6 41 S P T D M I R K A H A L S R P 1 56 W W M C S R RG K D I S W N F 1 48 K A H A L S R P W W M C S R R −5 213P1F11 v.2:HLA-DRB1*1101 15-mers 6 L H V Y S T V E G P T P F Q D 22 42 P T D M I RK A H A L S R P W 21 40 T S P T D M I R K A H A L S R 20 53 S R P W W MC S R R G K D I S 19 54 R P W W M C S R R G K D I S W 19 15 P T P F Q DP L Y L P S E A P 16 39 D T S P T D M I R K A H A L S 16 52 L S R P W WM C S R R G K D T 15 56 W W M C S R R G K D I S W N F 15 46 I R K A H AL S R P W W M C S 14 3 T D A L H V Y S T V E G P T P 13 18 F Q D P L Y LP S E A P P N P 12 19 Q D P L Y L P S E A P P N P P 12 21 P L Y L P S EA P P N P P L W 12 31 N P P L W N S Q D T S P T D M 12 49 A H A L S R PW W M C S R R G 12 20 D P L Y L P S E A P P N P P L 10 32 P P L W N S QD T S P T D M I 10 5 A L H V Y S T V E G P T P F Q 8 14 G P T P F Q D PL Y L P S E A 8 38 Q D T S P T D M I R K A H A L 8 44 D M I R K A H A LS R P W W M 8 2 Y T D A L H V Y S T V E G P T 7 4 D A L H V Y S T V E GP T P F 6 9 Y S T V E G P T P F Q D P L Y 6 10 S T V E G P T P F Q D P LY L 6 16 T P F Q D P L Y L P S E A P P 6 17 P F Q D P L Y L P S E A P PN 6 22 L Y L P S E A P P N P P L W N 6 26 S E A P P N P P L W N S Q D T6 28 A P P N P P L W N S Q D T S P 6 30 P N P P L W N S Q D T S P T D 643 T D M I R K A H A L S R P W W 6 55 P W W M C S R R G K D I S W N 6 7H V Y S T V E G P T P F Q D P 3 12 V E G P T P F Q D P L Y L P S 3 36 NS Q D T S P T D M I R K A H TABLE XIXC, part 3: MHC Class II 15-meranalysis of 213P1F11 v.3 (aa 1-146). 213P1F11 v.3: HLA-DRB1*0101 15-mers4 P K V Y T I Q A C R G A T L P 30 3 K P K V Y I I Q A C R G A T L 25 6V Y I I Q A C R G A T L P S P 24 11 A C R G A T L P S P F P Y L S 22 7 YT I Q A C R G A T L P S P F 18 8 I I Q A C R G A T L P S P F P 14 10 Q AC R G A T L P S P F P Y L 14 9 I Q A C R G A T L P S P F P Y 10 5 K V YI I Q A C R G A T L P S 8 12 C R G A T L P S P F P Y L S L 8 2 A K P K VY I I Q A C R G A T 7 1 R A K P K V Y I I Q A C R G A 1 213P1F11 v.3:HLA-DRB1*0301 (DR17) 15-mers 6 V Y I I Q A C R G A T L P S P 19 5 K V YI I Q A C R G A T L P S 18 12 C R G A T L P S P F P Y L S L 11 3 K P K VY I I Q A C R G A T L 10 10 Q A C R G A T L P S P F P Y L 9 2 A K P K VY I I Q A C R G A T 8 1 R A K P K V Y I I Q A C R G A 3 7 Y I I Q A C RG A T L P S P F 2 4 P K V Y I I Q A C R G A T L P 1 8 I I Q A C R G A TL P S P F P 1 9 I Q A C R G A T L P S P F P Y 1 11 A C R G A T L P S P FP Y L S 1 213P1F11 v.3: HLA-DRB1*0401 (DR4Dw4) 15-mers 5 K V Y I I Q A CR G A T L P S 26 4 P K V Y I I Q A C R G A T L P 16 3 K P K V Y I I Q AC R G A T L 14 6 V Y I I Q A C R G A T L P S P 14 2 A K P K V Y I I Q AC R G A T 12 8 I I Q A C R G A T L P S P F P 12 11 A C R G A T L P S P FP Y L S 12 9 I Q A C R G A T L P S P F P Y 6 7 Y I I Q A C R G A T L P SP F -5 213P1F11 v.3: HLA-DRB1*1101 15-mers 3 K P K V Y I T Q A C R G A TL 20 4 P K V Y I I Q A C R G A T L P 17 5 K V Y I I Q A C R G A T L P S14 11 A C R G A T L P S P F P Y L S 12 7 Y I I Q A C R G A T L P S P F 72 A K P K V Y I I Q A C R G A T 6 TABLE XIXC, part 4: MHC Class II15-mer analysis of 213P1F11 v.4 (aa 1-321). 213P1F11 v.4: HLA-DRB1*010115-mers 63 G G G V G D I V G R D L S I S 31 75 S I S F R N S E T S A S EE E 27 4 C Q E Y D K S L S V Q P E K R 26 31 T F R L K E E Q G R A F R GS 26 59 Q E V F G G G V G D I V G R D 26 55 P R E T Q E V F G G G V G DI 24 73 D L S I S F R N S E T S A S E 23 67 G D I V G R D L S I S F R NS 22 10 S L S V Q P E K R T G L R D E 19 18 R T G L R D E N G E C G Q TF 18 36 E E Q G R A F R G S S V H Q K 18 64 G G V G D I V G R D L S I SF 18 21 L R D E N G E C G Q T F R L K 17 58 T Q E V F G G G V G D I V GR 17 66 V G D I V G R D L S I S F R N 17 29 G Q T F R L K E E Q G R A FR 16 44 G S S V H Q K L V N D P R E T 16 8 D K S L S V Q P E K R T G L R15 41 A F R G S S V H Q K L V N D P 15 50 K L V N D P R E T Q E V F G G15 70 V G R D L S I S F R N S E T S 15 2 G K C Q E Y D K S L S V Q P E14 23 D E N G E C G Q T F R L K E E 14 7 Y D K S L S V Q P E K R T G L13 57 E T Q E V F G G G V G D I V G 13 39 G R A F R G S S V H Q K L V N12 85 A S E E E K Y D M S G A R L A 12 30 Q T F R L K E E Q G R A F R G11 34 L K E E Q G R A F R G S S V H 11 71 G R D L S I S F R N S E T S A11 12 S V Q P E K R T G L R D E N G 10 45 S S V H Q K L V N D P R E T Q10 49 Q K L V N D P R E T Q E V F G 10 68 D T V G R D L S I S F R N S E10 5 Q E Y D K S L S V Q P E K R T 9 15 P E K R T G L R D E N G E C G 940 R A F R G S S V H Q K L V N D 9 48 H Q K L V N D P R E T Q E V F 9 53N D P R E T Q E V F G G G V G 9 56 R E T Q E V F G G G V G D I V 9 74 LS I S F R N S E T S A S E E 9 82 E T S A S E E E K Y D M S G A 9 1 M G KC Q E Y D K S L S V Q P 8 28 C G Q T F R L K E E Q G R A F 8 33 R L K EE Q G R A F R G S S V 8 35 K E E Q G R A F R G S S V H Q 8 37 E Q G R AF R G S S V H Q K L 8 46 S V H Q K L V N D P R E T Q E 8 51 L V N D P RE T Q E V F G G G 8 65 G V G D I V G R D L S I S F R 8 77 S F R N S E TS A S E E E K Y 8 83 T S A S E E E K Y D M S G A R 8 24 E N G E C G Q TF R L K E E Q 7 32 F R L K E E Q G R A F R G S S 7 43 R G S S V H Q K LV N D P R E 7 47 V H Q K L V N D P R E T Q E V 7 60 E V F G G G V G D IV G R D L 7 69 I V G R D L S I S F R N S E T 7 76 I S F R N S E T S A SE E E K 7 86 S E E E K Y D M S G A R L A L 7 11 L S V Q P E K R T G L RD E N 6 38 Q G R A F R G S S V H Q K L v 6 78 F R N S E T S A S E E E KY D 6 9 K S L S V Q P E K R T G L R D 3 13 V Q P E K R T G L R D E N G E3 16 E K R T G L R D E N G E C G Q 3 19 T G L R D E N G E C G Q T F R 354 D P R E T Q E V F G G G V G D 3 14 Q P E K R T G L R D E N G E C 2 22R D E N G E C G Q T F R L K E 2 27 E C G Q T F R L K E E Q G R A 2 52 VN D P R E T Q E V F G G G v 2 61 V F G G G V G D I V G R D L S 2 80 N SE T S A S E E E K Y D M S 2 81 S E T S A S E E E K Y D M S G 2 6 E Y D KS L S V Q P E K R T G 1 17 K R T G L R D E N G E C G Q T 1 20 G L R D EN G E C G Q T F R L 1 25 N G E C G Q T F R L K E E Q G 1 26 G E C G Q TF R L K E E Q G R 1 62 F G G G V G D I V G R D L S I 1 79 R N S E T S AS E E E K Y D M 1 213P1F11 v.4: HLA-DRB1*0301 (DR17) 15-mers 67 G D I VG R D L S I S F R N S 29 48 H Q K L V N D P R E T Q E V F 28 10 S L S VQ P E K R T G L R D E 26 31 T F R L K E E Q G R A F R G S 21 17 K R T GL R D E N G E C G Q T 19 29 G Q T F R L K E E Q G R A F R 18 63 G G G VG D I V G R D L S I S 18 8 D K S L S V Q P E K R T G L R 17 71 G R D L SI S F R N S E T S A 17 49 Q K L V N D P R E T Q E V F G 16 80 N S E T SA S E E E K Y D M S 16 51 L V N D P R E T Q E V F G G G 14 2 G K C Q E YD K S L S V Q P E 12 44 G S S V H Q K L V N D P R E T 12 86 S E E E K YD M S G A R L A L 12 18 R T G L R D E N G E C G Q T F 11 40 R A F R G SS V H Q K L V N D 11 58 T Q E V F G G G V G D I V G R 11 62 F G G G V GD I V G R D L S I 11 66 V G D I V G R D L S I S F R N 11 75 S I S F R NS E T S A S E E E 11 39 G R A F R G S S V H Q K L V N 10 73 D L S I S FR N S E T S A S E 10 21 L R D E N G E C G Q T F R L K 9 30 Q T F R L K EE Q G R A F R G 9 32 F R L K E E Q G R A F R G S S 9 52 V N D P R E T QE V F G G G V 9 79 R N S E T S A S E E E K Y D M 9 1 M G K C Q E Y D K SL S V Q P 8 9 K S L S V Q P E K R T G L R D 8 14 Q P E K R T G L R D E NG E C 8 16 E K R T G L R D E N G E C G Q 8 19 T G L R D E N G E C G Q TF R 8 22 R D E N G E C G Q T F R L K E 8 23 D E N G E C G Q T F R L K EE 8 25 N G E C G Q T F R L K E E Q G 8 27 E C G Q T F R L K E E Q G R A8 41 A F R G S S V H Q K L V N D P 8 59 Q E V F G G G V G D I V G R D 864 G G V G D I V G R D L S I S F 8 72 R D L S I S F R N S E T S A S 8 81S E T S A S E E E K Y D M S G 8 82 E T S A S E E E K Y D M S G A 8 6 E YD K S L S V Q P E K R T G 7 28 C G Q T F R L K E E Q G R A F 7 42 F R GS S V H Q K L V N D P R 7 74 L S I S F R N S E T S A S E E 7 35 K E E QG R A F R G S S V H Q 6 45 S S V H Q K L V N D P R E T Q 6 70 V G R D LS I S F R N S E T S 5 5 Q E Y D K S L S V Q P E K R T 4 7 Y D K S L S VQ P E K R T G L 4 43 R G S S V H Q K L V N D P R E 4 50 K L V N D P R ET Q E V F G G 3 57 E T Q E V F G G G V G D I V G 3 4 C Q E Y D K S L S VQ P E K R 2 11 L S V Q P E K R T G L R D E E 2 13 V Q P E K R T G L R DE N G E 2 15 P E K R T G L R D E N G E C G 2 38 Q G R A F R G S S V H QK L V 2 46 S V H Q K L V N D P R E T Q E 2 47 V H Q K L V N D P R E T QE V 2 65 G V G D I V G R D L S I S F R 2 68 D I V G R D L S I S F R N SE 2 76 I S F R N S E T S A S E E E K 2 77 S F R N S E T S A S E E E K Y2 83 T S A S E E E K Y D M S G A R 2 3 K C Q E Y D K S L S V Q P E K 112 S V Q P E K R T G L R D E N G 1 20 G L R D E N G E C G Q T F R L 1 24E N G E C G Q T F R L K E E Q 1 36 E E Q G R A F R G S S V H Q K 1 37 EQ G R A F R G S S V H Q K L 1 53 N D P R E T Q E V F G G G V G 1 54 D PR E T Q E V F G G G V G D 1 55 P R E T Q E V F G G G V G D I 1 56 R E TQ E V F G G G V G D I v 1 60 E V F G G G V G D I V G R D L 1 61 V F G GG V G D I V G R D L S 1 69 I V G R D L S I S F R N S E T 1 84 S A S E EE K Y D M S G A R L 1 213P1F11 v.4: HLA-DRB1*0401 (DR4Dw4) 15-mers 10 SL S V Q P E K R T G L R D E 26 48 H Q K L V N D P R E T Q E V F 26 75 SI S F R N S E T S A S E E E 22 63 G G G V G D I V G R D L S I S 20 67 GD I V G R D L S I S F R N S 20 2 G K C Q E Y D K S L S V Q P E 18 30 Q TF R L K E E Q C R A F R G 18 35 K E E Q G R A F R G S S V H Q 18 41 A FR G S S V H Q K L V N D P 18 64 G G V G D I V G R D L S I S F 18 72 R DL S I S F R N S E T S A S 18 4 C Q E Y D K S L S V Q P E K R 16 39 G R AF R G S S V H Q K L V N 16 59 Q E V F G G G V G D I V G R D 16 73 D L SI S F R N S E T S A S E 15 8 D K S L S V Q P E K R T G L R 14 18 R T G LR D E N G E C G Q T F 14 31 T F R L K E E Q G R A F R G S 14 58 T Q E VF G G G V G D I V G R 14 71 G R D L S I S F R N S E T S A 14 6 E Y D K SL S V Q P E K R T G 12 14 Q P E K R T G L R D E N G E C 12 17 K R T G LR D E N G E C G Q T 12 23 D E N G E C G Q T F R L K E E 12 36 E E Q G RA F R G S S V H Q K 12 38 Q G R A F R G S S V H Q K L V 12 40 R A F R GS S V H Q K L V N D 12 45 S S V H Q K L V N D P R E T Q 12 51 L V N D PR E T Q E V F G G G 12 55 P R E T Q E V F G G G V G D I 12 69 I V G R DL S I S F R N S E T 12 70 V G R D L S I S F R N S E T S 12 76 I S F R NS E T S A S E E E K 12 79 R N S E T S A S E E E K Y D M 12 82 E T S A SE E E K Y D M S G A 12 83 T S A S E E E K Y D M S G A R 12 86 S E E E KY D M S G A R L A L 12 66 V G D I V G R D L S I S F R N 9 49 Q K L V N DP R E T Q E V F G 8 50 K L V N D P R E T Q E V F G G 7 1 M G K C Q E Y DK S L S V Q P 6 5 Q E Y D K S L S V Q P E K R T 6 7 Y D K S L S V Q P EK R T G L 6 15 P E K R T G L R D E N G E C G 6 19 T G L R D E N G E C GQ T F R 6 20 G L R D E N G E C G Q T F R L 6 21 L R D E N G E C G Q T FR L K 6 22 R D E N G E C G Q T F R L K E 6 24 E N G E C G Q T F R L K EE Q 6 25 N G E C G Q T F R L K E E Q G 6 26 G E C G Q T F R L K E E Q GR 6 28 C G Q T F R L K E E Q G R A F 6 32 F R L K E E Q G R A F R G S S6 42 F R G S S V H Q K L V N D P R 6 46 S V H Q K L V N D P R E T Q E 647 V H Q K L V N D P R E T Q E V 6 54 D P R E T Q E V F G G G V G D 6 56R E T Q E V F G G G V G D I V 6 60 E V F G G G V G D I V G R D L 6 62 FG G G V G D I V G R D L S I 6 65 G V G D I V G R D L S T S F R 6 68 D IV G R D L S I S F R N S E 6 74 L S I S F R N S E T S A S E E 6 78 F R NS E T S A S E E E K Y D 6 81 S E T S A S E E E K Y D M S G 6 85 A S E EE K Y D M S G A R L A 6 29 G Q T F R L K E E Q G R A F R 5 44 G S S V HQ K L V N D P R E T 3 3 K C Q E Y D K S L S V Q P E K 1 11 L S V Q P E KR T G L R D E N 1 27 E C G Q T F R L K E E Q G R A 1 34 L K E E Q G R AF R G S S V H 1 37 E Q G R A F R G S S V H Q K L 1 12 S V Q P E K R T GL R D E N G -5 16 E K R T G L R D E N G E C G Q -5 84 S A S E E E K Y DM S G A R L -5 213P1F11 v.4: HLA-DRB1*1101 15-mers 64 G G V G D I V G RD L S 1S F 21 4 C Q E Y D K S L S V Q P E K R 16 75 S I S F R N S E T SA S E E E 16 1 M G K C Q E Y D K S L S V Q P 15 9 K S L S V Q P E K R TG L R D 15 63 G G G V G D I V G R D L S I S 15 10 S L S V Q P E K R T GL R D E 14 15 P E K R T G L R D E N G E C G 14 35 K E E Q G R A F R G SS V H Q 14 48 H Q K L V N D P R E T Q E V F 14 71 G R D L S I S F R N SE T S A 14 28 C G Q T F R L K E E Q G R A F 13 59 Q E V F G G G V G D IV G R D 13 60 E V F G G G V G D I V G R D L 13 66 V G D I V G R D L S IS F R N 13 70 V G R D L S I S F R N S E T S 13 18 R T G L R D E N G E CG Q T F 12 44 G S S V H Q K L V N D P R E T 12 73 D L S I S F R N S E TS A S E 12 40 R A F R G S S V H Q K L V N D 11 27 E C G Q T F R L K E EQ G R A 10 29 G Q T F R L K E E Q G R A F R 10 39 G R A F R G S S V H QK L V N 10 42 F R G S S V H Q K L V N D P R 10 54 D P R E T Q E V F G GG V G D 10 8 D K S L S V Q P E K R T G L R 9 25 N G E C G Q T F R L K EE Q G 9 14 Q P E K R T G L R D E N G E C 8 30 Q T F R L K E E Q G R A FR G 8 32 F R L K E E Q G R A F R G S S 8 33 R L K E E Q G R A F R G S SV 8 45 S S V H Q K L V N D P R E T Q 8 46 S V H Q K L V N D P R E T Q E8 56 R E T Q E V F G G G V G D I V 8 82 E T S A S E E E K Y D M S G A 87 Y D K S L S V Q P E K R T G L 7 31 T F R L K E E Q G R A F R G S 7 34L K E E Q G R A F R G S S V H 7 41 A F R G S S V H Q K L V N D P 7 58 TQ E V F G G G V G D I V G R 7 74 L S I S F R N S E T S A S E E 7 5 Q E YD K S L S V Q P E K R T 6 49 Q K L V N D P R E T Q E V F G 6 52 V N D PR E T Q E V F G G G V 6 53 N D P R E T Q E V F G G G V G 6 55 P R E T QE V F G G G V G D I 6 67 G D I V G R D L S I S F R N S 6 68 D I V G R DL S I S F R N S E 6 83 T S A S E E E K Y D M S G A R 6 84 S A S E E E KY D M S G A R L 6 85 A S E E E K Y D M S G A R L A 6 6 E Y D K S L S V QP E K R T G 2 12 S V Q P E K R T G L R D E N G 2 23 D E N G E C G Q T FR L K E E 2 24 E N G E C G Q T F R L K E E Q 2 47 V H Q K L V N D P R ET Q E V 2 62 TABLE XIXC, part 5: MHC Class II 15-mer analysis of 2131F11v.5 (aa 1-242) 213P1F11 v.5: HLA-DRB1*0101 15-mers 8 A R L A L I L R V TK A R E G 21 11 A L I L R V T K A R E G S E E 19 2 K Y D M S G A R L A LI L R V 16 3 Y D M S G A R L A L T L R V T 16 9 R L A L I L R V T K A RE G S 16 7 G A R L A L I L R V T K A R E 15 10 L A L I L R V T K A R E GS E 14 5 M S G A R L A L I L R V T K A 11 12 L I L R V T K A R E G S E ED 11 13 I L R V T K A R E C S E E D L 11 14 L R V T K A R E G S E E D LD 10 6 S G A R L A L I L R V T K A R 9 1 E K Y D M S G A R L A L I L R 84 D M S G A R L A L I L R V T K 8 15 R V T K A R E G S E E D L D A 7213P1F11 v.5: HLA-DRB1*0301 (DR17) 15-mers 7 G A R L A L I L R V T K A RE 19 10 L A L I L R V T I C A R E G S E 19 1 E K Y D M S G A R L A L I LR 17 13 I L R V T K A R E G S E E D L 17 9 R L A L I L R V T K A R E G S13 2 K Y D N S G A R L A L T L R V 12 11 A L I L R V T K A R E G S E E12 3 Y D M S G A R L A L I L R V T 10 12 L I L R V T K A R E G S E E D 75 M S G A R L A L I L R V T K A 4 8 A R L A L I L R V T K A R E G 3 6 SG A R L A L T L R V T K A R 2 14 L R V T K A R E G S E E D L D 2 4 D M SG A R L A L I L R V T K 1 15 R V T K A R E G S E E D L D A 1 213P1F11v.5: HLA-DRB1*0401 (DR4Dw4) 15-mers 7 G A R L A L I L R V T K A R E 26 2K Y D M S G A R L A L I L R V 20 10 L A L I L R V T K A R E G S E 14 13I L R V T K A R E G S E E D L 14 1 E K Y D M S G A R L A L I L R 12 5 MS G A R L A L I L R V T K A 12 6 S G A R L A L I L R V T K A R 12 8 A RL A L I L R V T K A R E G 12 15 R V T K A R E G S E E D L D A 12 9 R L AL I L R V T K A R E G S 9 11 A L I L R V T K A R E G S E E 8 12 L I L RV T K A R E G S E E D 7 4 D M S G A R L A L I L R V T K 6 3 Y D M S G AR L A L I L R V T 1 14 L R V T K A R E G S E E D L D −5 213P1F11 v.5:HLA-DRB1*1101 15-mers 10 L A L I L R V T K A R E G S E 22 7 G A R L A LI L R V T K A R E 20 11 A L I L R V T K A R E G S E E 14 12 L I L R V TK A R E G S E E D 14 8 A R L A L I L R V T K A R E G 13 1 E K Y D M S GA R L A L I L R 8 6 S G A R L A L I L R V T K A R 8 9 R L A L I L R V TK A R E G S 8 13 I L R V T K A R E G S E E D L 8 2 K Y D M S G A R L A LI L R V 7 4 D M S G A R L A L I L R V T K 7 TABLE XIXC, part 6: MHCClass II 15-mer analysis of 2131F11 v.6 (aa 1-242). 213P1F11 v.6:HLA-DRB1*0101 15-mers 2 D G E M V K L E N L F E A M N 20 3 G E M V K L EN L F E A M N N 18 9 E N L F E A M N N K N C Q A L 17 12 F E A M N N K NC Q A L R A K 17 14 A M N N K N C Q A L R A K P K 17 5 M V K L E N L F EA M N N K N 16 6 V K L E N L F E A M N N K N C 11 8 L E N L F E A M N NK N C Q A 9 1 E D G E M V K L E N L F E A M 8 4 E M V K L E N L F E A MN N K 8 11 L F E A M N N K N C Q A L R A 8 15 M N N K N C Q A L R A K PK V 8 13 E A M N N K N C Q A L R A K P 3 7 K L E N L F E A M N N K N C Q1 10 N L F E A M N N K N C Q A L R 1 213P1F11 v.6: HLA-DRB1*0301 (DR17)15-mers 12 F E A M N N K N C Q A L R A K 20 2 D G E H V K L E N L F E AM N 19 8 L E N L F E A M N N K N C Q A 19 1 E D G E M V K L E N L F E AM 17 5 M V K L E N L F E A M N N K N 17 9 E N L F E A M N N K N C Q A L15 3 G E M V K L E N L F E A M N N 12 10 N L F E A M N N K N C Q A L R 813 E A M N N K N C Q A L R A K P 8 11 L F E A M N N K N C Q A L R A 7 4E M V K L E N L F E A M N N K 5 7 K L E N L F E A M N N K N C Q 4 6 V KL E N L F E A M N N K N C 3 14 A M N N K N C Q A L R A K P K 2 213P1F11v.6: HLA-DRB 1*0401 (DR4Dw4) 15-mers 8 L E N L F E A M N N K N C Q A 262 D G E M V K L E N L F E A M N 20 3 G E M V K L E N L F E A M N H 20 5M V K L E N L F E A M N N K N 20 9 E N L F E A M N N K N C Q A L 16 6 VK L E N L F E A M N N K N C 12 7 K L E N L F E A M N N K N C Q 12 11 L FE A M N N K N C Q A L R A 12 12 F E A M N N K N C Q A L R A K 9 4 E M VK L E N L F E A M N N K 6 10 N L F E A M N H K N C Q A L R 6 13 E A M NN K N C Q A L R A K P 6 14 A M N N K N C Q A L R A K P K 6 15 M N N K NC Q A L R A K P K V 6 1 E D G E M V K L E N L F E A M -5 213P1F11 v.6:HLA-DRB1*1101 15-mers 9 E N L F E A M N N K N C Q A L 16 2 D G E M V K LE N L F E A M N 12 3 G E M V K L E N L F E A M N N 12 5 M V K L E N L FE A M N N K N 12 8 L E N L F E A M N N K N C Q A 8 10 N L F E A M N N KN C Q A L R 8 14 A M N N K N C Q A L R A K P K 8 11 L F E A M N N K N CQ A L R A 6 12 F E A M N N K N C Q A L R A K 6 1 E D G E M V K L E N L FE A M 2 13 E A M N N K N C Q A L R A K P 1

[0772] TABLE XX Frequently Occurring Motifs avrg. % Name identityDescription Potential Function zf-C2H2 34% Zinc finger, C2H2 Nucleicacid-binding type protein functions as transcription factor, nuclearlocation probable cytochrome_b 68% Cytochrome b(N- membrane bound Nterminal)/b6/petB oxidase, generate superoxide ig 19% Immunoglobulindomains are one domain hundred amino acids long and include a conservedintradomain disulfide bond. WD40 18% WD domain, G-beta tandem repeats ofrepeat about 40 residues, each containing a Trp-Asp motif. Function insignal transduction and protein interaction PDZ 23% PDZ domain mayfunction in targeting signaling molecules to sub- membranous sites LRR28% Leucine Rich Repeat short sequence motifs involved in protein-protein interactions pkinase 23% Protein kinase domain conservedcatalytic core common to both serine/threonine and tyrosine proteinkinases contain- ing an ATP binding site and a catalytic site PH 16% PHdomain pleckstrin homology involved in intracellular signaling or asconstituents of the cyto skeleton EGF 34% EGF-like domain 30-40 amino-acid long found in the extracellular domain of membrane- bound proteinsor in secreted proteins rvt 49% Reverse transcriptase (RNA-dependent DNApolymerase) ank 25% Ank repeat Cytoplasmic protein, associates integralmembrane proteins to the cytoskeleton oxidored_ql 32% NADH- membraneassociated. Ubiquinone/plastoquin Involved in proton one (complex I),translocation various chains membrane across the membrane efand 4% EFhand calcium-binding domain, consists of a12 residue loop flanked onboth sides by a 12 residue alpha-helical domain rvp 79% Retroviralaspartyl Aspartyl or acid protease proteases, centered on a catalyticaspartyl residue Collagen 42% Collagen triple helix extracellular repeat(20 copies) structural proteins involved in formation of connectivetissue. The sequence consists of the G-X-Y and the polypeptide chainsforms a triple helix. fn3 20% Fibronectin type III Located in the extra-domain cellular ligand-binding region of receptors and is about 200amino acid residues long with two pairs of cysteines involved indisulfide bonds 7tm_1 19% 7 transmembrane seven hydro- receptor(rhodopsin phobic transmembrane family) regions, with the N-terminuslocated extracellularly while the C-terminus is cytoplasmic. Signalthrough G proteins

[0773] TABLE XXI Motifs and Post-translational Modifications of 213P1F11A) Post-translational Modifications of 213P1F11-v.1 Tyrosine sulfationsite. 5-19 rsleeekYdmsgarl Protein kinase C phosphorylation site 51-53TmK 196-198 TkR 210-212 TrR. 234-236 TlR Casein kinase IIphosphorylation site 6-9 SleE 32-35 SeeD 74-77 SreD 161-164 TytD 170-173StvE 190-193 TlvD 227-230 TnpE Tyrosine kinase phosphorylation site 5-12RsleEek.Y N-myristoylation site 16-21 GArlAL Bipartite nuclear targetingsequence 211-227 RRmaeaelvqegkarkt B) Post-translational Modificationsof 213P1F11-v.2 Tyrosine sulfation site. 5-19 rsleeekYdmsgarl Proteinkinase C phosphorylation site. 51-53 TmK 220-222 SrR Casein kinase IIphosphorylation site. 6-9 SleE 32-35 SeeD 74-77 SreD 161-164 TytD170-173 StvE 201-204 SptD Tyrosine kinase phosphorylation site 5-12RsleEek.Y N-myristoylation site 16-21 GArlAL

[0774] TABLE XXII Protein Properties of 213P1F11 Bioinformatic ProgramURL Outcome 213P1F11-v.1 ORF ORF finder 728 Protein length 242Transmembrane TM Pred http://www.ch.embnet.orgl No TM region HMMTophttp://www.enzim.hu/hmmtop/ No TM Sosui http://www.genome.ad.jp/SOSui NoTM TMHMM http://www.cbs.dtu.dk/services/TMHMM TMP = 0 Signal PeptideSignal P http://www.cbs.dtu.dk/services/SignalP Non-Secretory Protein pIpI/MW tool http://www.expasy.ch/tools/ pI: 5.44 Molecular weight pI/MWtool http://www.expasy.ch/tools/ 28.0 kDa Localization PSORThttp://psort.nibb.ac.jp/ endoplasmic reticulum 55.0% lysosome 19% PSORTII http://psort.nibb.ac.jp/ 56.5%: cytoplasmic 21.7%: nuclear MotifsPfam http://www.sanger.ac.uk/Pfam/ Interleukin-1 converting enzyme (ICE)Prints http://www.biochem.ucl.ac.uk/ Interleukin-1B converting enzymeBlocks http://www.blocks.fhcrc.org/ ICE-like protease (caspase) p20dom >213P1F11-v.2 ORF ORF finder 692 Protein length 230 Transmembrane TMPred http://www.ch.embnet.org/ No TM region HMMTophttp://www.enzim.hu/hmmtop/ No TM Sosui http://www.genome.ad.jp/SOSui/Soluble Protein. 0 TMHMM http://www.cbs.dtu.dk/services/TMHMM No TMSignal Peptide Signal P http://www.cbs.dtu.dk/services/SignalP/Non-Secretory Protein pI pI/MW tool http://www.expasy.ch/tools/  4.94Molecular weight pI/MW tool http://www.expasy.ch/tools/ 26.5 kDaLocalization PSORT http://psort.nibb.ac.jp/ endoplasmic reticulum 55.0%lysosome 19% PSORT II http://psort.nibb.ac.jp/ 39.1%: nuclear 30.4%:mitochondrial Motifs Pfam http://www.sanger.ac.uk/Pfam/ Interleukin-1converting enzyme (ICE) Prints http://www.biochem.ucl.ac.uk/Interleukin-1 B converting enzyme Blocks http://www.blocks.fbcrc.org/ICE-like protease (caspase) p20 dom 213P1F11-v.3 ORF ORF finder 440Protein length 146 Transmembrane TM Pred http://www.ch.embnet.org/ No TMregion HMMTop http://www.enzim.hu/hmmtop/ No TM Sosuihttp://www.genome.ad.jp/SOSui/ No TM TMHMMhttp://www.cbs.dtu.dk/dservices/TMHMM No TM Signal Peptide Signal Phttp://www.cbs.dtu.dk/services/SignalP/ Non-Secretory Protein pI pI/MWtool http://www.expasy.ch/tools/ Theoretical pI: 5.06 Molecular weightpI/MW tool http://www.expasy.ch/tools/ Theoretical MW: 16977.4Localization PSORT http://psort.nibb.ac.jp/ endoplasmic reticulum 55.0%lysosome 19% PSORT II http://psort.nibb.ac.jp/ 60.9%: cytoplasmic 17.4%:nuclear Motifs Pfam http://www.sanger.ac.uk/Pfam/ Interleukin-1converting enzyme (ICE) Prints http://www.biochem.ucl.ac.uk/Interleukin-1B converting enzyme Blocks http://www.blocks.fhcrc.org/ICE-like protease (caspase) p20 dom 213P1F11-v.4 Protein length 321Transmembrane TM Pred http://www.ch.embnet.org/ TM = 0 region HMMTophttp://www.enzim.hu/hmmtop/ TM = 0 Sosui http://sosui..ac.jp/ SolubleProtein. TM = 0 TMHMM http://www.cbs.dtu.dk/services/TMHMM TMP = SignalPeptide Signal P http://www.cbs.dtu.dk/services/SignalP/ pI pI/MW toolhttp://www.expasy.ch/tools/ Theoretical pI: 5.42 Molecular weight pI/MWtool http://www.expasy.ch/tools/ Theoretical MW: 36398.04 LocalizationPSORT http://psort.nibb.ac.jp/ endoplasmic reticulum (membrane)Certainty = 0.760 lysosome (lumen) Certainty = 0.100 microbody(peroxisome) Certainty =  0.300 mitochondrial matrix space Certainty = 0.100 PSORT II http://psort.nibb.ac.jp/ 47.8%: cytoplasmic 39.1%:nuclear 13.0%: vacuolar  8.7%: mitochondrial Motifs Pfamhttp://www.sanger.ac.uk/Pfam/ Interleukin-1 converting enzyme (ICE) p20& p10 domain Prints http://www.biochem.ucl.ac.uk/ Interleukin-1Bconverting enzyme Blocks http://www.blocks.fhcrc.org/ ICE-like protease(caspase) p20 domain

[0775] TABLE XXIIIA Exon compositions of 213P1F11 v.1 Exon Number StartEnd Exon 1 1 357 Exon 2 358 430 Exon 3 431 580 Exon 4 581 806 Exon 5 807923 Exon 6 924 1027 Exon 7 1028 3336

[0776] TABLE XXIIIB Exon compositions of 213P1F11 v.4 Exon Number StartEnd Exon 1 1 119 Exon 2 120 212 Exon 3 213 264 Exon 4 265 414 Exon 5 415640 Exon 6 641 757 Exon 7 758 861 Exon 8 862 966

[0777] TABLE XXIVA Nucleotide sequence of transcript variant 213P1F11v.2 ctgactcatt tagactctct gcctaggcca cctttgccag agggagtccc ctcagccttg 60cgatcactca tcccattggc gttggctcca tttccacacc acagctgtgt gccaagggtg 120tgtcatgagg tttcttgagt gacagaaaac tcaccgacaa taaagggcca ggtgattgtg 180ccacccgatt catagaccag gcttctcagg agaaaccccg ggagattcca cactgtcagc 240cccttctcca agatcagtac gtgggcctga ctcctcctcg gtgcccagct cagtattggc 300aactaggaga gtagtgagat tgaacttggc cttgaggaac agctgcctct agagttggat 360cagacaaggg tgctgagagc cgggactcac aaccaaagga gaaatgagca atccgcggtc 420tttggaagag gagaaatatg atatgtcagg tgcccgcctg gccctaatac tgtgtgtcac 480caaagcccgg gaaggttccg aagaagacct ggatgctctg gaacacatgt ttcggcagct 540gagattcgaa agcaccatga aaagagaccc cactgccgag caattccagg aagagctgga 600aaaattccag caggccatcg attcccggga agatcccgtc agttgtgcct tcgtggtact 660catggctcac gggagggaag gcttcctcaa gggagaagat ggggagatgg tcaagctgga 720gaatctcttc gaggccctga acaacaagaa ctgccaggcc ctgcgagcta agcccaaggt 780gtacatcata caggcctgtc gaggagaaca aagggacccc ggtgaaacag taggtggaga 840tgagattgtg atggtcatca aagacagccc acaaaccatc ccaacataca cagatgcctt 900gcacgtttat tccacggtag agggacccac gcccttccag gatcccctct acctaccctc 960tgaagctccc ccgaacccac ctctctggaa ttcccaggat acatcgccta ccgacatgat 1020cagaaaggct catgctttat ccagaccctg gtggatgtgt tcacgaagag gaaaggacat 1080atcttggaac ttctgacaga ggtgacccgg cggatggcag aagcagagct ggttcaagaa 1140ggaaaagcaa ggaaaacgaa ccctgaaatc caaagcaccc tccggaaacg gctgtatctg 1200cagtagaagt agaaagacca ggaggagctt tccttccagc attctttctg tctcacagaa 1260atttagaggc agctcttacc tctccccaag atcttctgtt cccaaggcca aatggcaccc 1320agtttctttt ccatcacacc cttcatgcag gtcctcctgt ccttattaga gcaagccagc 1380caaaacttag cacaaggcat ggtggcaaca ttaacatcac ctccctcagg ctggactttc 1440tatctttatt aatgcaaccg aagagaccta agagtgcatt cacttatccc actttctgtt 1500cctgtggtct tctttctccc atgaagcaga aactggataa agctcaagat tttccataga 1560caaaccaaag cccactcatc ccctcctacc ccaatccaac ctctgctggc tcctgcatct 1620cacttggagg tcaaacctcc tcctgaggcc aatgcattcc caacttccag ttctttcctt 1680taccctggag agttagtaag gtaagaacca ttctttctct ccaaaaccac tcctccttgg 1740ctggcaagtt ggtgtcctaa ctccgttctc ttcctagctc atggcctctc tagataataa 1800agttgtctcc tcctttctgg atctcttcct cctaacaccc ctcccctgaa accctggact 1860ctgccctctc tccaagaaaa tccatctatt caactattct tgcattcaat tactctaaat 1920gagagcgtgt tggagctatg gcaaattccc tgttgtcacc ttgctatttt gcagacaaca 1980taatatttaa cctctcataa ccagagaggt taaataattt gtcaaatgca atacagtaag 2040acagaggcaa ggacaaggtt tgacttccag cccagcctct tttccacaac ctgctaaatc 2100ctgatccatc tgaaaacttt tctaattagt gaagatgact aataaaaatt ttccctatct 2160ccaaggtagg agctttctgg aagtttctag aaattttcaa taaccaccag ccaaggttac 2220ctccaggtaa ccttgcagca ccaggctgga agtcagatcg gcttcactat cttccaactc 2280tacagcctgt atctctccat ccccagcttt gacctttcct gctcaagtaa cctacgggca 2340catccagcgt cactaaaaac tcagggcttt tcttcccggt tactcctcca agcgttccct 2400ggtatcctca acctcagatc ccaggttcag atttctgcag tcaatctatg acccctctct 2460tcttgcatcc ttcatatgcc accagacacc atgcccagtc cagcctgatt ttgaaacaac 2520tttcatgccg gtcttctctt ccctgacatg ttactgtcca ggctcaagtc ctcagcttct 2580catatctgca tctttgcaac caacttcctc ccttgcctct ctgcttttcc atcccacttt 2640tcatgtgtcc tccataccat ctataacagt gatctccctg gaacactcaa gaagacacaa 2700cataccatat tatttaaaga ccagggtact ggacagtggc tcacacctgt attcccgact 2760ttgagagtct gaagcgggag gatcacttga ggccaggagt taagagacca gcctgggcaa 2820cacagcaaga ccctgtctct aaaaaaaaaa attaattaac tgggtatggt ggcacatgcc 2880tgtagtccca gctactcagg aggctgaggt gggaggatga cttgagccca ggagtttgag 2940gctgcaagga gctatgatca tgccagtgca tcccagctct aggtgagaca gtgagatccg 3000gtctccaaaa taaatcaatc aatcaaataa agaccaaagt caaaccgcac atcaggatct 3060ctcacaccct tccaattttg ccatctacca gcacttagct aaacccatct cccatctctt 3120ccaccatgaa ttcactcttt caaaaaggct aatgtcttct tactcaccct tgcctctaag 3180cctttgctat caccatttcc cccaagctgg agggccctcc ctctcccttt acccctcttc 3240cactacctcc cacccctact ttttccagaa agccatttcc tctctttttt ctgattgatc 3300cttccctctc acccaggatt agatgctgga aatgaccact tctggagggc agggaacaag 3360cccttaatct gcataatgag tgttcaataa acagttgtca aactttgaaa  3410

[0778] TABLE XXIVB Nucleotide sequence of transcript variant 213P1F11v.3 ctgactcatt tagactctct gcctaggcca cctttgccag agggagtccc ctcagccttg 60cgatcactca tcccattggc gttggctcca tttccacacc acagctgtgt gccaagggtg 120tgtcatgagg tttcttgagt gacagaaaac tcaccgacaa taaagggcca ggtgattgtg 180ccacccgatt catagaccag gcttctcagg agaaaccccg ggagattcca cactgtcagc 240cccttctcca agatcagtac gtgggcctga ctcctcctcg gtgcccagct cagtattggc 300aactaggaga gtagtgagat tgaacttggc cttgaggaac agctgcctct agagttggat 360cagacaaggg tgctgagagc cgggactcac aaccaaagga gaaatgagca atccgcggtc 420tttggaagag gagaaatatg atatgtcagg tgcccgcctg gccctaatac tgtgtgtcac 480caaagcccgg gaaggttccg aagaagacct ggatgctctg gaacacatgt ttcggcagct 540gagattcgaa agcaccatga aaagagaccc cactgccgag caattccagg aagagctgga 600aaaattccag caggccatcg attcccggga agatcccgtc agttgtgcct tcgtggtact 660catggctcac gggagggaag gcttcctcaa gggagaagat ggggagatgg tcaagctgga 720gaatctcttc gaggccctga acaacaagaa ctgccaggcc ctgcgagcta agcccaaggt 780gtacatcata caggcctgtc gaggagccac cctgcccagc ccctttcctt acctttctct 840ctgactttgc ctcctcctct tcttgttgtt tcagaacaaa gggaccccgg tgaaacagta 900ggtggagatg agattgtgat ggtcatcaaa gacagcccac aaaccatccc aacatacaca 960gatgccttgc acgtttattc cacggtagag ggatacatcg cctaccgaca tgatcagaaa 1020ggctcatgct ttatccagac cctggtggat gtgttcacga agaggaaagg acatatcttg 1080gaacttctga cagaggtgac ccggcggatg gcagaagcag agctggttca agaaggaaaa 1140gcaaggaaaa cgaaccctga aatccaaagc accctccgga aacggctgta tctgcagtag 1200aagtagaaag accaggagga gctttccttc cagcattctt tctgtctcac agaaatttag 1260aggcagctct tacctctccc caagatcttc tgttcccaag gccaaatggc acccagtttc 1320ttttccatca cacccttcat gcaggtcctc ctgtccttat tagagcaagc cagccaaaac 1380ttagcacaag gcatggtggc aacattaaca tcacctccct caggctggac tttctatctt 1440tattaatgca accgaagaga cctaagagtg cattcactta tcccactttc tgttcctgtg 1500gtcttctttc tcccatgaag cagaaactgg ataaagctca agattttcca tagacaaacc 1560aaagcccact catcccctcc taccccaatc caacctctgc tggctcctgc atctcacttg 1620gaggtcaaac ctcctcctga ggccaatgca ttcccaactt ccagttcttt cctttaccct 1680ggagagttag taaggtaaga accattcttt ctctccaaaa ccactcctcc ttggctggca 1740agttggtgtc ctaactccgt tctcttccta gctcatggcc tctctagata ataaagttgt 1800ctcctccttt ctggatctct tcctcctaac acccctcccc tgaaaccctg gactctgccc 1860tctctccaag aaaatccatc tattcaacta ttcttgcatt caattactct aaatgagagc 1920gtgttggagc tatggcaaat tccctgttgt caccttgcta ttttgcagac aacataatat 1980ttaacctctc ataaccagag aggttaaata atttgtcaaa tgcaatacag taagacagag 2040gcaaggacaa ggtttgactt ccagcccagc ctcttttcca caacctgcta aatcctgatc 2100catctgaaaa cttttctaat tagtgaagat gactaataaa aattttccct atctccaagg 2160taggagcttt ctggaagttt ctagaaattt tcaataacca ccagccaagg ttacctccag 2220gtaaccttgc agcaccaggc tggaagtcag atcggcttca ctatcttcca actctacagc 2280ctgtatctct ccatccccag ctttgacctt tcctgctcaa gtaacctacg ggcacatcca 2340gcgtcactaa aaactcaggg cttttcttcc cggttactcc tccaagcgtt ccctggtatc 2400ctcaacctca gatcccaggt tcagatttct gcagtcaatc tatgacccct ctcttcttgc 2460atccttcata tgccaccaga caccatgccc agtccagcct gattttgaaa caactttcat 2520gccggtcttc tcttccctga catgttactg tccaggctca agtcctcagc ttctcatatc 2580tgcatctttg caaccaactt cctcccttgc ctctctgctt ttccatccca cttttcatgt 2640gtcctccata ccatctataa cagtgatctc cctggaacac tcaagaagac acaacatacc 2700atattattta aagaccaggg tactggacag tggctcacac ctgtattccc gactttgaga 2760gtctgaagcg ggaggatcac ttgaggccag gagttaagag accagcctgg gcaacacagc 2820aagaccctgt ctctaaaaaa aaaaattaat taactgggta tggtggcaca tgcctgtagt 2880cccagctact caggaggctg aggtgggagg atgacttgag cccaggagtt tgaggctgca 2940aggagctatg atcatgccag tgcatcccag ctctaggtga gacagtgaga tccggtctcc 3000aaaataaatc aatcaatcaa ataaagacca aagtcaaacc gcacatcagg atctctcaca 3060cccttccaat tttgccatct accagcactt agctaaaccc atctcccatc tcttccacca 3120tgaattcact ctttcaaaaa ggctaatgtc ttcttactca cccttgcctc taagcctttg 3180ctatcaccat ttcccccaag ctggagggcc ctccctctcc ctttacccct cttccactac 3240ctcccacccc tactttttcc agaaagccat ttcctctctt ttttctgatt gatccttccc 3300tctcacccag gattagatgc tggaaatgac cacttctgga gggcagggaa caagccctta 3360atctgcataa tgagtgttca ataaacagtt gtcaaacttt gaaa  3404

[0779] TABLE XXIVC Nucleotide sequence of transcript variant 213P1F11v.4 atggggaaat gccaagagta tgacaaaagt ctgtctgtgc agccagagaa gagaacagga 60ctcagagatg agaatggaga atgtggacag acattcagac tcaaggaaga gcaagggagg 120gctttcaggg gaagttcagt ccaccagaag ctggtgaatg acccacggga gacacaggaa 180gtttttgggg gcggagtggg ggacattgtg ggacgggatc tcagtattag cttcagaaac 240tctgagacct ctgcaagtga ggaggagaaa tatgatatgt caggtgcccg cctggcccta 300atactgtgtg tcaccaaagc ccgggaaggt tccgaagaag acctggatgc tctggaacac 360atgtttcggc agctgagatt cgaaagcacc atgaaaagag accccactgc cgagcaattc 420caggaagagc tggaaaaatt ccagcaggcc atcgattccc gggaagatcc cgtcagttgt 480gccttcgtgg tactcatggc tcacgggagg gaaggcttcc tcaagggaga agatggggag 540atggtcaagc tggagaatct cttcgaggcc ctgaacaaca agaactgcca ggccctgcga 600gctaagccca aggtgtacat catacaggcc tgtcgaggag aacaaaggga ccccggtgaa 660acagtaggtg gagatgagat tgtgatggtc atcaaagaca gcccacaaac catcccaaca 720tacacagatg ccttgcacgt ttattccacg gtagagggat acatcgccta ccgacatgat 780cagaaaggct catgctttat ccagaccctg gtggatgtgt tcacgaagag gaaaggacat 840atcttggaac ttctgacaga ggtgacccgg cggatggcag aagcagagct ggttcaagaa 900ggaaaagcaa ggaaaacgaa ccctgaaatc caaagcaccc tccggaaacg gctgtatctg 960cagtag  966

[0780] TABLE XXVA Nucleotide sequence alignment of 213P1F11 v.1 and213P1F11 v.2 213P1F11v.1CTGACTCATTTAGACTCTCTGCCTAGGCCACCTTTGCCAGAGGGAGTCCCCTCAGCCTTG 60213P1F11v.2 CTGACTCATTTAGACTCTCTGCCTAGGCCACCTTTGCCAGAGGGAGTCCCCTCAGCCTTG60 ************************************************************213P1F11v.1 CGATCACTCATCCCATTGGCGTTGGCTCCATTTCCACACCACAGCTGTGTGCCAAGGGTG120 213P1F11v.2CGATCACTCATCCCATTGCCGTTGGCTCCATTTCCACACCACAGCTGTGTGCCAAGGGTG 120************************************************************ 213P1F11v.1TGTCATGAGGTTTCTTGAGTGACAGAAAACTCACCGACAATAAAGGGCCAGGTGATTGTG 180213P1F11v.2 TGTCATGAGGTTTCTTGAGTGACAGAAAACTCACCGACAATAAAGGGCCAGGTGATTGTG180 ************************************************************213P1F11v.1 CCACCCGATTCATAGACCAGGCTTCTCAGGAGAAACCCCGGGAGATTCCACACTGTCAGC240 213P1F11v.2CCACCCGATTCATAGACCAGGCTTCTCAGGAGAAACCCCGGGAGATTCCACACTGTCAGC 240************************************************************ 213P1F11v.1CCCTTCTCCAAGATCAGTACGTGGGCCTGACTCCTCCTCGGTGCCCAGCTCAGTATTGGC 300213P1F11v.2 CCCTTCTCCAAGATCAGTACGTGGGCCTGACTCCTCCTCGGTGCCCAGCTCAGTATTGGC300 ************************************************************213P1F11v.1 AACTAGGAGAGTAGTGAGATTGAACTTGGCCTTGAGGAACAGCTGCCTCTAGAGTTGGAT360 213P1F11v.2AACTAGGAGAGTAGTGAGATTGAACTTGGCCTTGAGGAACAGCTGCCTCTAGAGTTGGAT 360************************************************************ 213P1F11v.1CAGACAAGGGTGCTGAGAGCCGGGACTCACAACCAAAGGAGAAATGAGCAATCCGCGGTC 420213P1F11v.2 CAGACAAGGGTGCTGAGAGCCGGGACTCACAACCAAAGGAGAAATGAGCAATCCGCGGTC420 ************************************************************213P1F11v.1 TTTGGAAGAGGAGAAATATGATATGTCAGGTGCCCGCCTGGCCCTAATACTGTGTGTCAC480 213P1F11v.2TTTGGAAGAGGAGAAATATGATATGTCAGGTGCCCGCCTGGCCCTAATACTGTGTGTCAC 480************************************************************ 213P1F11v.1CAAAGCCCGGGAAGGTTCCGAAGAAGACCTGGATGCTCTGGAACACATGTTTCGGCAGCT 540213P1F11v.2 CAAAGCCCGGGAAGGTTCCGAAGAAGACCTGGATGCTCTGGAACACATGTTTCGGCAGCT540 ************************************************************213P1F11v.1 GAGATTCGAAAGCACCATGAAAAGAGACCCCACTGCCGAGCAATTCCAGGAAGAGCTGGA600 213P1F11v.2GAGATTCGAAAGCACCATGAAAAGAGACCCCACTGCCGAGCAATTCCAGGAAGAGCTGGA 600************************************************************ 213P1F11v.1AAAATTCCAGCAGGCCATCGATTCCCGGGAAGATCCCGTCAGTTGTGCCTTCGTGGTACT 660213P1F11v.2 AAAATTCCAGCAGGCCATCGATTCCCGGGAAGATCCCGTCAGTTGTGCCTTCGTGGTACT660 ************************************************************213P1F11v.1 CATGGCTCACGGGAGGGAAGGCTTCCTCAAGGGAGAAGATGGGGAGATGGTCAAGCTGGA720 213P1F11v.2CATGGCTCACGGGAGGGAAGGCTTCCTCAAGGGAGAAGATGGGGAGATGGTCAAGCTGGA 720************************************************************ 213P1F11v.1GAATCTCTTCGAGGCCCTGAACAACAAGAACTGCCAGGCCCTGCGAGCTAAGCCCAAGGT 780213P1F11v.2 GAATCTCTTCGAGGCCCTGAACAACAAGAACTGCCAGGCCCTGCGAGCTAAGCCCAAGGT780 ************************************************************213P1F11v.1 GTACATCATACAGGCCTGTCGAGGAGAACAAAGGGACCCCGGTGAAACAGTAGGTGGAGA840 213P1F11v.2GTACATCATACAGGCCTGTCGAGGAGAACAAAGGGACCCCGGTGAAACAGTAGGTGGAGA 840************************************************************ 213P1F11v.1TGAGATTGTGATGGTCATCAAAGACAGCCCACAAACCATCCCAACATACACAGATGCCTT 900213P1F11v.2 TGAGATTGTGATGGTCATCAAAGACAGCCCACAAACCATCCCAACATACACAGATGCCTT900 ************************************************************213P1F11v.1 GCACGTTTATTCCACGGTAGAGGGA-----------------------------------925 213P1F11v.2GCACGTTTATTCCACGGTAGAGGGACCCACGCCCTTCCAGGATCCCCTCTACCTACCCTC 960************************* 213P1F11v.1---------------------------------------TACATCGCCTACCGACATGAT 946213P1F11v.2 TGAAGCTCCCCCGAACCCACCTCTCTGGAATTCCCAGGATACATCGCCTACCGACATGAT1020                                        *********************213P1F11v.1 CAGAAAGGCTCATGCTTTATCCAGACCCTGGTGGATGTGTTCACGAAGAGGAAAGGACAT1006 213P1F11v.2CAGAAAGGCTCATGCTTTATCCAGACCCTGGTGGATGTGTTCACGAAGAGGAAAGGACAT 1080************************************************************ 213P1F11v.1ATCTTGGAACTTCTGACAGAGGTGACCCGGCGGATGGCAGAAGCAGAGCTGGTTCAAGAA 1066213P1F11v.2 ATCTTGGAACTTCTGACAGAGGTGACCCGGCGGATGGCAGAAGCAGAGCTGGTTCAAGAA1140 ************************************************************213P1F11v.1 GGAAAAGCAAGGAAAACGAACCCTGAAATCCAAAGCACCCTCCGGAAACGGCTGTATCTG1126 213P1F11v.2GGAAAAGCAAGGAAAACGAACCCTGAAATCCAAAGCACCCTCCGGAAACGGCTGTATCTG 1200************************************************************ 213P1F11v.1CAGTAGAAGTAGAAAGACCAGGAGGAGCTTTCCTTCCAGCATTCTTTCTGTCTCACAGAA 1186213P1F11v.2 CAGTAGAAGTAGAAAGACCAGGAGGAGCTTTCCTTCCAGCATTCTTTCTGTCTCACAGAA1260 ************************************************************213P1F11v.1 ATTTAGAGGCAGCTCTTACCTCTCCCCAAGATCTTCTGTTCCCAAGGCCAAATGGCACCC1246 213P1F11v.2ATTTAGAGGCAGCTCTTACCTCTCCCCAAGATCTTCTGTTCCCAAGGCCAAATGGCACCC 1320************************************************************ 213P1F11v.1AGTTTCTTTTCCATCACACCCTTCATGCAGGTCCTCCTGTCCTTATTAGAGCAAGCCAGC 1366213P1F11v.2 AGTTTCTTTTCCATCACACCCTTCATGCAGGTCCTCCTGTCCTTATTAGAGCAAGCCAGC1380 ************************************************************213P1F11v.1 CAAAACTTAGCACAAGGCATGGTGGCAACATTAACATCACCTCCCTCAGGCTGGACTTTC1366 213P1F11v.2CAAAACTTAGCACAAGGCATGGTGGCAACATTAACATCACCTCCCTCAGGCTGGACTTTC 1440************************************************************ 213P1F11v.1TATCTTTATTAATGCAACCGAAGAGACCTAAGAGTGCATTCACTTATCCCACTTTCTGTT 1426213P1F11v.2 TATCTTTATTAATGCAACCGAAGAGACCTAAGAGTGCATTCACTTATCCCACTTTCTGTT1500 ************************************************************213P1F11v.1 CCTGTGGTCTTCTTTCTCCCATGAAGCAGAAACTGGATAAAGCTCAAGATTTTCCATAGA1486 213P1F11v.2CCTGTGGTCTTCTTTCTCCCATGAAGCAGAAACTGGATAAAGCTCAAGATTTTCCATAGA 1560************************************************************ 213P1F11v.1CAAACCAAAGCCCACTCATCCCCTCCTACCCCAATCCAACCTCTGCTGGCTCCTGCATCT 1546213P1F11v.2 CAAACCAAAGCCCACTCATCCCCTCCTACCCCAATCCAACCTCTGCTGGCTCCTGCATCT1620 ************************************************************213P1F11v.1 CACTTGGAGGTCAAACCTCCTCCTGAGGCCAATGCATTCCCAACTTCCAGTTCTTTCCTT1606 213P1F11v.2CACTTGGAGGTCAAACCTCCTCCTGAGGCCAATGCATTCCCAACTTCCAGTTCTTTCCTT 1680************************************************************ 213P1F11v.1TACCCTGGAGAGTTAGTAAGGTAAGAACCATTCTTTCTCTCCAAAACCACTCCTCCTTGG 1666213P1F11v.2 TACCCTGGAGAGTTAGTAAGGTAAGAACCATTCTTTCTCTCCAAAACCACTCCTCCTTGG1740 ************************************************************213P1F11v.1 CTGGCAAGTTGGTGTCCTAACTCCGTTCTCTTCCTAGCTCATGGCCTCTCTAGATAATAA1726 213P1F11v.2CTGGCAAGTTGGTGTCCTAACTCCGTTCTCTTCCTAGCTCATGGCCTCTCTAGATAATAA 1800************************************************************ 213P1F11v.1AGTTGTCTCCTCCTTTCTGGATCTCTTCCTCCTAACACCCCTCCCCTGAAACCCTGGACT 1786213P1F11v.2 AGTTGTCTCCTCCTTTCTGGATCTCTTCCTCCTAACACCCCTCCCCTGAAACCCTGGACT1860 ************************************************************213P1F11v.1 CTGCCCTCTCTCCAAGAAAATCCATCTATTCAACTATTCTTGCATTCAATTACTCTAAAT1846 213P1F11v.2CTGCCCTCTCTCCAAGAAAATCCATCTATTCAACTATTCTTGCATTCAATTACTCTAAAT 1920************************************************************ 213P1F11v.1GAGAGCGTGTTGGAGCTATGGCAAATTCCCTGTTGTCACCTTGCTATTTTGCAGACAACA 1906213P1F11v.2 GAGAGCGTGTTGGAGCTATGGCAAATTCCCTGTTGTCACCTTGCTATTTTGCAGACAACA1980 ************************************************************213P1F11v.1 TAATATTTAACCTCTCATAACCAGAGAGGTTAAATAATTTGTCAAATGCAATACAGTAAG1966 213p1F11v.2TAATATTTAACCTCTCATAACCAGAGAGGTTAAATAATTTGTCAAATGCAATACAGTAAG 2040************************************************************ 213P1F11v.1ACAGAGGCAAGGACAAGGTTTGACTTCCAGCCCAGCCTCTTTTCCACAACCTGCTAAATC 2026213P1F11v.2 ACAGAGGCAAGGACAAGGTTTGACTTCCAGCCCAGCCTCTTTTCCACAACCTGCTAAATC2100 ************************************************************213P1F11v.1 CTGATCCATCTGAAAACTTTTCTAATTAGTGAAGATGACTAATAAAAATTTTCCCTATCT2086 213P1F11v.2CTGATCCATCTGAAAACTTTTCTAATTAGTGAAGATGACTAATAAAAATTTTCCCTATCT 2160************************************************************ 213P1F11v.1CCAAGGTAGGAGCTTTCTGGAAGTTTCTAGAAATTTTCAATAACCACCAGCCAAGGTTAC 2146213P1F11v.2 CCAAGGTAGGAGCTTTCTGGAAGTTTCTAGAAATTTTCAATAACCACCAGCCAAGGTTAC2220 ************************************************************213P1F11v.1 CTCCAGGTAACCTTGCAGCACCAGGCTGGAAGTCAGATCGGCTTCACTATCTTCCAACTC2206 213P1F11v.2CTCCAGGTAACCTTGCAGCACCAGGCTGGAAGTCAGATCGGCTTCACTATCTTCCAACTC 2280************************************************************ 213P1F11v.1TACAGCCTGTATCTCTCCATCCCCAGCTTTGACCTTTCCTGCTCAAGTAACCTACGGGCA 2266213P1F11v.2 TACAGCCTGTATCTCTCCATCCCCAGCTTTGACCTTTCCTGCTCAAGTAACCTACGGGCA2340 ************************************************************213P1F11v.1 CATCCAGCGTCACTAAAAACTCAGGGCTTTTCTTCCCGGTTACTCCTCCAAGCGTTCCCT2326 213P1F11v.2CATCCAGCGTCACTAAAAACTCAGGGCTTTTCTTCCCGGTTACTCCTCCAAGCGTTCCCT 2400************************************************************ 213P1F11v.1GGTATCCTCAACCTCAGATCCCAGGTTCAGATTTCTGCAGTCAATCTATGACCCCTCTCT 2386213P1F11v.2 GGTATCCTCAACCTCAGATCCCAGGTTCACATTTCTGCAGTCAATCTATGACCCCTCTCT2460 ************************************************************213P1F11v.1 TCTTGCATCCTTCATATGCCACCAGACACCATGCCCAGTCCAGCCTGATTTTGAAACAAC2446 213P1F11v.2TCTTGCATCCTTCATATGCCACCAGACACCATGCCCAGTCCAGCCTGATTTTGAAACAAC 2520************************************************************ 213P1F11v.1TTTCATGCCGGTCTTCTCTTCCCTGACATGTTACTGTCCAGGCTCAAGTCCTCAGCTTCT 2506213P1F11v.2 TTTCATGCCGGTCTTCTCTTCCCTGACATGTTACTGTCCAGGCTCAAGTCCTCAGCTTCT2580 ************************************************************213P1F11v.1 CATATCTGCATCTTTGCAACCAACTTCCTCCCTTGCCTCTCTGCTTTTCCATCCCACTTT2566 213P1F11v.2CATATCTGCATCTTTGCAACCAACTTCCTCCCTTGCCTCTCTGCTTTTCCATCCCACTTT 2640************************************************************ 213P1F11v.1TCATGTGTCCTCCATACCATCTATAACAGTGATCTCCCTGGAACACTCAAGAAGACACAA 2626213P1F11v.2 TCATGTGTCCTCCATACCATCTATAACAGTGATCTCCCTGGAACACTCAAGAAGACACAA2700 ************************************************************ **213P1F11v.1 CATACCATATTATTTAAAGACCAGGGTACTGGACAGTGGCTCACACCTGTATTCCCGACT2686 213P1F11v.2CATACCATATTATTTAAAGACCAGGGTACTGGACAGTGGCTCACACCTGTATTCCCGACT 2760************************************************************ 213P1F11v.1TTGAGAGTCTGAAGCGGGAGGATCACTTGAGGCCAGGAGTTAAGAGACCAGCCTGGGCAA 2746213P1F11v.2 TTGAGAGTCTGAAGCGGGAGGATCACTTGAGGCCAGGAGTTAAGAGACCAGCCTGGGCAA2820 ************************************************************213P1F11v.1 CACAGCAAGACCCTGTCTCTAAAAAAAAAAATTAATTAACTGGGTATGGTGGCACATGCC2806 213P1F11v.2CACAGCAAGACCCTGTCTCTAAAAAAAAAAATTAATTAACTGGGTATGGTGGCACATGCC 2880************************************************************ 213P1F11v.1TGTAGTCCCAGCTACTCAGGAGGCTGAGGTGGGAGGATGACTTGAGCCCAGGAGTTTGAG 2866213P1F11v.2 TGTAGTCCCAGCTACTCAGGAGGCTGAGGTGGGAGGATGACTTGAGCCCAGGAGTTTGAG2940 ************************************************************213P1F11v.1 GCTGCAAGGAGCTATGATCATGCCAGTGCATCCCAGCTCTAGGTGAGACAGTGAGATCCG2926 213P1F11v.2GCTGCAAGGAGCTATGATCATGCCAGTGCATCCCAGCTCTAGGTGAGACAGTGAGATCCG 3000************************************************************ 213P1F11v.1GTCTCCAAAATAAATCAATCAATCAAATAAAGACCAAAGTCAAACCGCACATCAGGATCT 2986213P1F11v.2 GTCTCCAAAATAAATCAATCAATCAAATAAAGACCAAAGTCAAACCGCACATCAGGATCT3060 ************************************************************213P1F11v.1 CTCACACCCTTCCAATTTTGCCATCTACCAGCACTTAGCTAAACCCATCTCCCATCTCTT3046 213P1F11v.2CTCACACCCTTCCAATTTTGCCATCTACCAGCACTTAGCTAAACCCATCTCCCATCTCTT 3120************************************************************ 213P1F11v.1CCACCATGAATTCACTCTTTCAAAAAGGCTAATGTCTTCTTACTCACCCTTGCCTCTAAG 3106213P1F11v.2 CCACCATGAATTCACTCTTTCAAAAAGGCTAATGTCTTCTTACTCACCCTTGCCTCTAAG3180 ************************************************************213P1F11v.1 CCTTTGCTATCACCATTTCCCCCAAGCTGGAGGGCCCTCCCTCTCCCTTTACCCCTCTTC3166 213P1F11v.2CCTTTGCTATCACCATTTCCCCCAAGCTGGAGGGCCCTCCCTCTCCCTTTACCCCTCTTC 3240************************************************************ 213P1F11v.1CACTACCTCCCACCCCTACTTTTTCCAGAAAGCCATTTCCTCTCTTTTTTCTGATTGATC 3226213P1F11v.2 CACTACCTCCCACCCCTACTTTTTCCAGAAAGCCATTTCCTCTCTTTTTTCTGATTGATC3300 ************************************************************213P1F11v.1 CTTCCCTCTCACCCAGGATTAGATGCTGGAAATGACCACTTCTGGAGGGCAGGGAACAAG3286 213P1F11v.2CTTCCCTCTCACCCAGGATTAGATGCTGGAAATGACCACTTCTGGAGGGCAGGGAACAAG 3360************************************************************ 213P1F11v.1CCCTTAATCTGCATAATGAGTGTTCAATAAACAGTTGTCAAACTTTGAAA  3336 213P1F11v.2CCCTTAATCTGCATAATGAGTGTTCAATAAACAGTTGTCAAACTTTGAAA  3410**************************************************

[0781] TABLE XXVB Nucleotide sequence alignment of 213P1F11 v.1 and213P1F11 v.3 213P1F11v.1CTGACTCATTTAGACTCTCTGCCTAGGCCACCTTTGCCAGAGGGAGTCCCCTCAGCCTTG 60213P1F11v.3 CTGACTCATTTAGACTCTCTGCCTAGGCCACCTTTGCCAGAGGGAGTCCCCTCAGCCTTG60 ************************************************************213P1F11v.1 CGATCACTCATCCCATTGGCGTTGGCTCCATTTCCACACCACAGCTGTGTGCCAAGGGTG120 213P1F11v.3CGATCACTCATCCCATTGGCGTTGGCTCCATTTCCACACCACAGCTGTGTGCCAAGGGTG 120************************************************************ 213P1F11v.1TGTCATGAGGTTTCTTGAGTGACAGAAAACTCACCGACAATAAAGGGCCAGGTGATTGTG 180213P1F11v.3 TGTCATGAGGTTTCTTGAGTGACAGAAAACTCACCGACAATAAAGGGCCAGGTGATTGTG180 ************************************************************213P1F11v.1 CCACCCGATTCATAGACCAGGCTTCTCAGGAGAAACCCCGGGAGATTCCACACTGTCAGC240 213P1F11v.3CCACCCGATTCATAGACCAGGCTTCTCAGGAGAAACCCCGGGAGATTCCACACTGTCAGC 240************************************************************ 213P1F11v.1CCCTTCTCCAAGATCAGTACGTGGGCCTGACTCCTCCTCGGTGCCCAGCTCAGTATTGGC 300213P1F11v.3 CCCTTCTCCAAGATCAGTACGTGGGCCTGACTCCTCCTCGGTGCCCAGCTCAGTATTGGC300 ************************************************************213P1F11v.1 AACTAGGAGAGTAGTGAGATTGAACTTGGCCTTGAGGAACAGCTGCCTCTAGAGTTGGAT360 213P1F11v.3AACTAGGAGAGTAGTGAGATTGAACTTGGCCTTGAGGAACAGCTGCCTCTAGAGTTGGAT 360************************************************************ 213P1F11v.1CAGACAAGGGTGCTGAGAGCCGGGACTCACAACCAAAGGAGAAATGAGCAATCCGCGGTC 420213P1F11v.3 CAGACAAGGGTGCTGAGAGCCGGGACTCACAACCAAAGGAGAAATGAGCAATCCGCGGTC420 ************************************************************213P1F11v.1 TTTGGAAGAGGAGAAATATGATATGTCAGGTGCCCGCCTGGCCCTAATACTGTGTGTCAC480 213P1F11v.3TTTGGAAGAGGAGAAATATGATATGTCAGGTGCCCGCCTGGCCCTAATACTGTGTGTCAC 480************************************************************ 213P1F11v.1CAAAGCCCGGGAAGGTTCCGAAGAAGACCTGGATGCTCTGGAACACATGTTTCGGCAGCT 540213P1F11v.3 CAAAGCCCGGGAAGGTTCCGAAGAAGACCTGGATGCTCTGGAACACATGTTTCGGCAGCT540 ************************************************************213P1F11v.1 GAGATTCGAAAGCACCATGAAAAGAGACCCCACTGCCGAGCAATTCCAGGAAGAGCTGGA600 213P1F11v.3GAGATTCGAAAGCACCATGAAAAGAGACCCCACTGCCGAGCAATTCCAGGAAGAGCTGGA 600************************************************************ 213P1F11v.1AAAATTCCAGCAGGCCATCGATTCCCGGGAAGATCCCGTCAGTTGTGCCTTCGTGGTACT 660213P1F11v.3 AAAATTCCAGCAGGCCATCGATTCCCGGGAAGATCCCGTCAGTTGTGCCTTCGTGGTACT660 ************************************************************213P1F11v.1 CATGGCTCACGGGAGGGAAGGCTTCCTCAAGGGAGAAGATGGGGAGATGGTCAAGCTGGA720 213P1F11v.3CATGGCTCACGGGAGGGAAGGCTTCCTCAAGGGAGAAGATGGGGAGATGGTCAAGCTGGA 720************************************************************ 213P1F11v.1GAATCTCTTCGAGGCCCTGAACAACAAGAACTGCCAGGCCCTGCGAGCTAAGCCCAAGGT 780213P1F11v.3 GAATCTCTTCGAGGCCCTGAACAACAAGAACTGCCAGGCCCTGCGAGCTAAGCCCAAGGT780 ************************************************************213P1F11v.1 GTACATCATACAGGCCTGTCGAGGAG----------------------------------806 213P1F11v.3GTACATCATACAGGCCTGTCGAGGAGCCACCCTGCCCAGCCCCTTTCCTTACCTTTCTCT 840************************** 213P1F11v.1----------------------------------AACAAAGGGACCCCGGTGAAACAGTA 832213P1F11v.3 CTGACTTTGCCTCCTCCTCTTCTTGTTGTTTCAGAACAAAGGGACCCCGGTGAAACAGTA900                                   **************************213P1F11v.1 GGTGGAGATGAGATTGTGATGGTCATCAAAGACAGCCCACAAACCATCCCAACATACACA892 213P1F11v.3GGTGGAGATGAGATTGTGATGGTCATCAAAGACAGCCCACAAACCATCCCAACATACACA 960************************************************************ 213P1F11v.1GATGCCTTGCACGTTTATTCCACGGTAGAGGGATACATCGCCTACCGACATGATCAGAAA 952213P1F11v.3 GATGCCTTGCACGTTTATTCCACGGTAGAGGGATACATCGCCTACCGACATGATCAGAAA1020 ************************************************************213P1F11v.1 GGCTCATGCTTTATCCAGACCCTGGTGGATGTGTTCACGAAGAGGAAAGGACATATCTTG1012 213P1F11v.3GGCTCATGCTTTATCCAGACCCTGGTGGATGTGTTCACGAAGAGGAAAGGACATATCTTG 1080************************************************************ 213P1F11v.1GAACTTCTGACAGAGGTGACCCGGCGGATGGCAGAAGCAGAGCTGGTTCAAGAAGGAAAA 1072213P1F11v.3 GAACTTCTGACAGAGGTGACCCGGCGGATGGCAGAAGCAGAGCTGGTTCAAGAAGGAAAA1140 ************************************************************213P1F11v.1 GCAAGGAAAACGAACCCTGAAATCCAAAGCACCCTCCGGAAACGGCTGTATCTGCAGTAG1132 213P1F11v.3GCAAGGAAAACGAACCCTGAAATCCAAAGCACCCTCCGGAAACGGCTGTATCTGCAGTAG 1200************************************************************ 213P1F11v.1AAGTAGAAAGACCAGGAGGAGCTTTCCTTCCAGCATTCTTTCTGTCTCACAGAAATTTAG 1192213P1F11v.3 AAGTAGAAAGACCAGGAGGAGCTTTCCTTCCAGCATTCTTTCTGTCTCACAGAAATTTAG1260 ************************************************************213P1F11v.1 AGGCAGCTCTTACCTCTCCCCAAGATCTTCTGTTCCCAAGGCCAAATGGCACCCAGTTTC1252 213P1F11v.3AGGCAGCTCTTACCTCTCCCCAAGATCTTCTGTTCCCAAGGCCAAATGGCACCCAGTTTC 1320************************************************************ 213P1F11v.1TTTTCCATCACACCCTTCATGCAGGTCCTCCTGTCCTTATTAGAGCAAGCCAGCCAAAAC 1312213P1F11v.3 TTTTCCATCACACCCTTCATGCAGGTCCTCCTGTCCTTATTAGAGCAAGCCAGCCAAAAC1380 ************************************************************213P1F11v.1 TTAGCACAAGGCATGGTGGCAACATTAACATCACCTCCCTCAGGCTGGACTTTCTATCTT1372 213P1F11v.3TTAGCACAAGGCATGGTGGCAACATTAACATCACCTCCCTCAGGCTGGACTTTCTATCTT 1440************************************************************ 213P1F11v.1TATTAATGCAACCGAAGAGACCTAAGAGTGCATTCACTTATCCCACTTTCTGTTCCTGTG 1432213P1F11v.3 TATTAATGCAACCGAAGAGACCTAAGAGTGCATTCACTTATCCCACTTTCTGTTCCTGTG1500 ************************************************************213P1F11v.1 GTCTTCTTTCTCCCATGAAGCAGAAACTGGATAAAGCTCAAGATTTTCCATAGACAAACC1492 213P1F11v.3GTCTTCTTTCTCCCATGAAGCAGAAACTGGATAAAGCTCAAGATTTTCCATAGACAAACC 1560************************************************************ 213P1F11v.1AAAGCCCACTCATCCCCTCCTACCCCAATCCAACCTCTGCTGGCTCCTGCATCTCACTTG 1552213P1F11v.3 AAAGCCCACTCATCCCCTCCTACCCCAATCCAACCTCTGCTGGCTCCTGCATCTCACTTG1620 ************************************************************213P1F11v.1 GAGGTCAAACCTCCTCCTGAGGCCAATGCATTCCCAACTTCCAGTTCTTTCCTTTACCCT1612 213P1F11v.3GAGGTCAAACCTCCTCCTGAGGCCAATGCATTCCCAACTTCCAGTTCTTTCCTTTACCCT 1680************************************************************ 213P1F11v.1GGAGAGTTAGTAAGGTAAGAACCATTCTTTCTCTCCAAAACCACTCCTCCTTGGCTGGCA 1672213P1F11v.3 GGAGAGTTAGTAAGGTAAGAACCATTCTTTCTCTCCAAAACCACTCCTCCTTGGCTGGCA1740 ************************************************************213P1F11v.1 AGTTGGTGTCCTAACTCCGTTCTCTTCCTAGCTCATGGCCTCTCTAGATAATAAAGTTGT1732 213P1F11v.3AGTTGGTGTCCTAACTCCGTTCTCTTCCTAGCTCATGGCCTCTCTAGATAATAAAGTTGT 1800************************************************************ 213P1F11v.1CTCCTCCTTTCTGGATCTCTTCCTCCTAACACCCCTCCCCTGAAACCCTGGACTCTGCCC 1792213P1F11v.3 CTCCTCCTTTCTGGATCTCTTCCTCCTAACACCCCTCCCCTGAAACCCTGGACTCTGCCC1860 ************************************************************213P1F11v.1 TCTCTCCAAGAAAATCCATCTATTCAACTATTCTTGCATTCAATTACTCTAAATGAGAGC1852 213P1F11v.3TCTCTCCAAGAAAATCCATCTATTCAACTATTCTTGCATTCAATTACTCTAAATGAGAGC 1920************************************************************ 213P1F11v.1GTGTTGGAGCTATGGCAAATTCCCTGTTGTCACCTTGCTATTTTGCAGACAACATAATAT 1912213P1F11v.3 GTGTTGGAGCTATGGCAAATTCCCTGTTGTCACCTTGCTATTTTGCAGACAACATAATAT1980 ************************************************************213P1F11v.1 TTAACCTCTCATAACCAGAGAGGTTAAATAATTTGTCAAATGCAATACAGTAAGACAGAG1972 213P1F11v.3TTAACCTCTCATAACCAGAGAGGTTAAATAATTTGTCAAATGCAATACAGTAAGACAGAG 2040************************************************************ 213P1F11v.1GCAAGGACAAGGTTTGACTTCCAGCCCAGCCTCTTTTCCACAACCTGCTAAATCCTGATC 2032213P1F11v.3 GCAAGGACAAGGTTTGACTTCCAGCCCAGCCTCTTTTCCACAACCTGCTAAATCCTGATC2100 ************************************************************213P1F11v.1 CATCTGAAAACTTTTCTAATTAGTGAAGATGACTAATAAAAATTTTCCCTATCTCCAAGG2092 213P1F11v.3CATCTGAAAACTTTTCTAATTAGTGAAGATGACTAATAAAAATTTTCCCTATCTCCAAGH 2160************************************************************ 213P1F11v.1TAGGAGCTTTCTGGAAGTTTCTAGAAATTTTCAATAACCACCAGCCAAGGTTACCTCCAG 2152213P1F11v.3 TAGGAGCTTTCTGGAAGTTTCTAGAAATTTTCAATAACCACCAGCCAAGGTTACCTCCAG2220 ************************************************************213P1F11v.1 GTAACCTTGCAGGACCAGGCTGGAAGTCAGATCGGCTTCACTATCTTCCAACTCTACAGC2212 213P1F11v.3GTAACCTTGCAGGACCAGGCTGGAAGTCAGATCGGCTTCACTATCTTCCAACTCTACAGC 2280************************************************************ 213P1F11v.1CTGTATCTCTCCATCCCCAGCTTTGACCTTTCCTGCTCAAGTAACCTACGGGCACATCCA 2272213P1F11v.3 CTGTATCTCTCCATCCCCAGCTTTGACCTTTCCTGCTCAAGTAACCTACGGGCACATCCA2340 ************************************************************213P1F11v.1 GCGTCACTAAAAACTCAGGGCTTTTCTTCCCGGTTACTCCTCCAAGCGTTCCCTGGTATC2332 213P1F11v.3GCGTCACTAAAAACTCAGGGCTTTTCTTCCCGGTTACTCCTCCAAGCGTTCCCTGGTATC 2400************************************************************ 213P1F11v.1CTCAACCTCAGATCCCAGGTTCAGATTTCTGCAGTCAATCTATGACCCCTCTCTTCTTGC 2392213P1F11v.3 CTCAACCTCAGATCCCAGGTTCAGATTTCTGCAGTCAATCTATGACCCCTCTCTTCTTGC2460 ************************************************************213P1F11v.1 ATCCTTCATATGCCACCAGACACCATGCCCAGTCCAGCCTGATTTTGAAACAACTTTCAT2452 213P1F11v.3ATCCTTCATATGCCACCAGACACCATGCCCAGTCCAGCCTGATTTTGAAACAACTTTCAT 2520************************************************************ 213P1F11v.1GCCGGTCTTCTCTTCCCTGACATGTTACTGTCCAGGCTCAAGTCCTCAGCTTCTCATATC 2512213P1F11v.3 GCCGGTCTTCTCTTCCCTGACATGTTACTGTCCAGGCTCAAGTCCTCAGCTTCTCATATC2580 ************************************************************213P1F11v.1 TGCATCTTTGCAACCAACTTCCTCCCTTGCCTCTCTGCTTTTCCATCCCACTTTTCATGT2572 213P1F11v.3TGCATCTTTGCAACCAACTTCCTCCCTTGCCTCTCTGCTTTTCCATCCCACTTTTCATGT 2640************************************************************ 213P1F11v.1GTCCTCCATACCATCTATAACAGTGATCTCCCTGGAACACTCAAGAAGACACAACATACC 2632213P1F11v.3 GTCCTCCATACCATCTATAACAGTGATCTCCCTGGAACACTCAAGAAGACACAACATACC2700 ************************************************************213P1F11v.1 ATATTATTTAAAGACCAGGGTACTGGACAGTGGCTCACACCTGTATTCCCGACTTTGACA2692 213P1F11v.3ATATTATTTAAAGACCAGGGTACTGGACAGTGGCTCACACCTGTATTCCCGACTTTGACA 2760************************************************************ 213P1F11v.1GTCTGAAGCGGGAGGATCACTTGAGGCCAGGAGTTAAGAGACCAGCCTGGGCAACACAGC 2752213P1F11v.3 GTCTGAAGCGGGAGGATCACTTGAGGCCAGGAGTTAAGAGACCAGCCTGGGCAACACAGC2820 ************************************************************213P1F11v.1 AAGACCCTGTCTCTAAAAAAAAAAATTAATTAACTGGGTATGGTGGCACATGCCTGTAGT2812 213P1F11v.3AAGACCCTGTCTCTAAAAAAAAAAATTAATTAACTGGGTATGGTGGCACATGCCTGTAGT 2880************************************************************ 213P1F11v.1CCCAGCTACTCAGGAGGCTGAGGTGGGAGGATGACTTGAGCCCAGGAGTTTGAGGCTGCA 2872213P1F11v.3 CCCAGCTACTCAGGAGGCTGAGGTGGGAGGATGACTTGAGCCCAGGAGTTTGAGGCTGCA2940 ************************************************************213P1F11v.1 AGGAGCTATGATCATGCCAGTGCATCCCAGCTCTAGGTGAGACAGTGAGATCCGGTCTCC2932 213P1F11v.3AGGAGCTATCATCATGCCAGTGCATCCCAGCTCTAGGTGAGACAGTGAGATCCGGTCTCC 3000************************************************************ 213P1F11v.1AAAATAAATCAATCAATCAAATAAAGACCAAAGTCAAACCGCACATCAGGATCTCTCACA 2992213P1F11v.3 AAAATAAATCAATCAATCAAATAAAGACCAAAGTCAAACCGCACATCAGGATCTCTCACA3060 ************************************************************213P1F11v.1 CCCTTCCAATTTTGCCATCTACCAGCACTTAGCTAAACCCATCTCCCATCTCTTCCACCA3052 213P1F11v.3CCCTTCCAATTTTGCCATCTACCAGCACTTAGCTAAACCCATCTCCCATCTCTTCCACCA 3120************************************************************ 213P1F11v.1TGAATTCACTCTTTCAAAAAGGCTAATGTCTTCTTACTCACCCTTGCCTCTAAGCCTTTG 3112213P1F11v.3 TGAATTCACTCTTTCAAAAAGGCTAATGTCTTCTTACTCACCCTTGCCTCTAAGCCTTTG3180 ************************************************************213P1F11v.1 CTATCACCATTTCCCCCAAGCTGGAGGGCCCTCCCTCTCCCTTTACCCCTCTTCCACTAC3172 213P1F11v.3CTATCACCATTTCCCCCAAGCTGGAGGGCCCTCCCTCTCCCTTTACCCCTCTTCCACTAC 3240************************************************************ 213P1F11v.1CTCCCACCCCTACTTTTTCCAGAAAGCCATTTCCTCTCTTTTTTCTGATTGATCCTTCCC 3232213P1F11v.3 CTCCCACCCCTACTTTTTCCAGAAAGCCATTTCCTCTCTTTTTTCTGATTGATCCTTCCC3300 ************************************************************213P1F11v.1 TCTCACCCAGGATTAGATGCTGGAAATGACCACTTCTGGAGGGCAGGGAACAAGCCCTTA3292 213P1F11v.3TCTCACCCAGGATTAGATGCTGGAAATGACCACTTCTGGAGGGCAGGGAACAAGCCCTTA 3360************************************************************ 213P1F11v.1ATCTGCATAATGAGTGTTCAATAAACAGTTGTCAAACTTTGAAA  3336 213P1F11v.3ATCTGCATAATGAGTGTTCAATAAACAGTTGTCAAACTTTGAAA  3404********************************************

[0782] TABLE XXVC Nucleotide sequence alignment of 213P1F11 v.1 and213P1F11 v.4 213P1F11v.1CTGACTCATTTAGACTCTCTGCCTAGGCCACCTTTGCCAGAGGGAGTCCCCTCAGCCTTG 60213P1F11v.4 ------------------------------------------------------------213P1F11v.1 CGATCACTCATCCCATTGGCGTTGGCTCCATTTCCACACCACAGCTGTGTGCCAAGGGTG120 213P1F11v.4------------------------------------------------------------ 213P1F11v.1TGTCATGAGGTTTCTTGAGTGACAGAAAACTCACCGACAATAAAGGGCCAGG-TGATTGT 179213P1F11v.4 ---------------------ATGGGGAAAT-GCCAAGAGTATGACAAAAGTCTGTCTGT38                      *  *  ** *  ** * * **       **  **  ***213P1F11v.1 GCCACCCGATTCATAGACCAGGCTTCTCAGGAGAAACCCCGGGAGATTCCACACTGTCAG239 213P1F11v.4GCAGCCAGAGA-AGAGAACAGGACTCAGAGATGAGAAT---GGAGAATGTGGACAGACA- 93**  ** **   * *** ****  **  **  ** *     ***** *    ** * ** 213P1F11v.1CCCCTTCTCCAAGATCAGTACGTGGGCCTGACTCCTCCTCGGTGCCCAGCTCAGTATTGG 299213P1F11v.4 TTCAGACTCAAGGAAGAGCAAGGGAC---GGCTTTCAGGGGAAGTTCAGTCCACCAGAAG150   *   *** * **  ** * * * *   * **       *  *  ***  **  *   *213P1F11v.1 CAACTAGGAGAGTAGTGAGATTGAACTTGGCCTTGAGGAACAGCTGCCTCTAGAGTTGGA359 213P1F11v.4CTGGTGAATGACCCACGGGA---GACAC-------AGGAA-----GTTTTTGGGGGCGGA 195*   *    **     * **    **         *****     *  * * * *  *** 213P1F11v.1TCAGACAAGGGTGCTGAGAGCCGGGA-CTCACAACCAAAGG-AGAAATGAGCAATCCGCG 417213P1F11v.4 GTGGG---GGACATTGTGGGACGGGATCTCAGTATTAGCTTCAGAAACTCTGAGACCTCT252    *    **    ** * * ***** ****  *  *     *****     *  ** * 213P1F11v.1 GTCTTTGGAAGAGGAGAAATATGATATGTCAGGTGCCCGCCTGGCCCTAATACTGTGTGT477 213P1F11v.4GCAAGTG-AGGAGGAGAAATATGATATGTCAGCTGCCCGCCTGGCCCTAATACTGTGTGT 311*    ** * ************************************************** 213P1F11v.1CACCAAAGCCCGGGAAGGTTCCGAAGAAGACCTGGATGCTCTGGAACACATGTTTCGGCA 537213P1F11v.4 CACCAAAGCCCGGGAAGGTTCCGAAGAAGACCTGGATGCTCTGGAACACATGTTTCGGCA371 ************************************************************213P1F11v.1 GCTGAGATTCGAAAGCACCATGAAAAGAGACCCCACTGCCGAGCAATTCCAGGAAGAGCT597 213P1F11v.4GCTGAGATTCGAAAGCACCATGAAAAGAGACCCCACTGCCGAGCAATTCCAGGAAGAGCT 431************************************************************ 213P1F11v.1GGAAAAATTCCAGCAGGCCATCGATTCCCGGGAAGATCCCGTCAGTTGTGCCTTCGTGGT 657213P1F11v.4 GGAAAAATTCCAGCAGGCCATCGATTCCCGGGAAGATCCCGTCAGTTGTGCCTTCGTGGT491 ************************************************************213P1F11v.1 ACTCATGGCTCACGGGAGGGAAGGCTTCCTCAAGGGAGAAGATGGGGAGATGGTCAAGCT717 213P1F11v.4ACTCATGGCTCACGGGAGGGAAGGCTTCCTCAAGGGAGAAGATGGGGAGATGGTCAAGCT 551************************************************************ 213P1F11v.1GGAGAATCTCTTCGAGGCCCTGAACAACAAGAACTGCCAGGCCCTGCGAGCTAAGCCCAA 777213P1F11v.4 GGAGAATCTCTTCGAGGCCCTGAACAACAAGAACTGCCAGGCCCTGCGAGCTAAGCCCAA611 ************************************************************213P1Fl1v.1 GGTGTACATCATACAGGCCTGTCGAGGAGAACAAAGGGACCCCGGTGAAACAGTAGGTGG837 213P1F11v.4GGTGTACATCATACAGGCCTGTCGAGGAGAACAAAGGGACCCCGGTGAAACAGTAGGTGG 671************************************************************ 213P1F11v.1AGATGAGATTGTGATGGTCATCAAAGACAGCCCACAAACCATCCCAACATACACAGATGC 897213P1F11v.4 AGATGAGATTGTGATGGTCATCAAAGACAGCCCACAAACCATCCCAACATACACAGATGC731 ************************************************************213P1F11v.1 CTTGCACGTTTATTCCACGGTAGAGGGATACATCGCCTACCGACATGATCAGAAAGGCTC957 213P1F11v.4CTTGCACGTTTATTCCACGGTAGAGGGATACATCGCCTACCGACATGATCAGAAAGGCTC 791************************************************************ 213P1F11v.1ATGCTTTATCCAGACCCTGGTGGATGTGTTCACGAAGAGGAAAGGACATATCTTGGAACT 1017213P1F11v.4 ATGCTTTATCCAGACCCTGGTGGATGTGTTCACGAAGAGGAAAGGACATATCTTGGAACT851 ************************************************************213P1F11v.1 TCTGACAGAGGTGACCCGGCGGATGGCAGAAGCAGAGCTGGTTCAAGAAGGAAAAGCAAG1077 213P1F11v.4TCTGACAGAGGTGACCCGGCGGATGGCAGAAGCAGAGCTGGTTCAAGAAGGAAAAGCAAG 911************************************************************ 213P1F11v.1GAAAACGAACCCTGAAATCCAAAGCACCCTCCGGAAACGGCTGTATCTGCAGTAGAAGTA 1137213P1F11v.4 GAAAACGAACCCTGAAATCCAAAGCACCCTCCGGAAACGGCTGTATCTGCAGTAG-----966 ******************************************************* 213P1F11v.1GAAAGACCAGGAGGAGCTTTCCTTCCAGCATTCTTTCTGTCTCACAGAAATTTAGAGGCA 1197213P1F11v.4 ------------------------------------------------------------213P1F11v.1 GCTCTTACCTCTCCCCAAGATCTTCTGTTCCCAAGGCCAAATGGCACCCAGTTTCTTTTC1257 213P1F11v.4------------------------------------------------------------ 213P1F11v.1CATCACACCCTTCATGCAGGTCCTCCTGTCCTTATTAGAGCAAGCCAGCCAAAACTTAGC 1317213P1F11v.4 ------------------------------------------------------------213P1F11v.1 ACAAGGCATGGTGGCAACATTAACATCACCTCCCTCAGGCTGGACTTTCTATCTTTATTA1377 213P1F11v.4------------------------------------------------------------ 213P1F11v.1ATGCAACCGAAGAGACCTAAGAGTGCATTCACTTATCCCACTTTCTGTTCCTGTGGTCTT 1437213P1F11v.4 ------------------------------------------------------------213P1F11v.1 CTTTCTCCCATGAAGCAGAAACTGGATAAAGCTCAAGATTTTCCATAGACAAACCAAAGC1497 213P1F11v.4------------------------------------------------------------ 213P1F11v.1CCACTCATCCCCTCCTACCCCAATCCAACCTCTGCTGGCTCCTGCATCTCACTTGGAGGT 1557213P1F11v.4 ------------------------------------------------------------213P1F11v.1 CAAACCTCCTCCTGAGGCCAATGCATTCCCAACTTCCAGTTCTTTCCTTTACCCTGGAGA1617 213P1F11v.4------------------------------------------------------------ 213P1F11v.1GTTAGTAAGGTAAGAACCATTCTTTCTCTCCAAAACCACTCCTCCTTGGCTGGCAAGTTG 1677213P1F11v.4 ------------------------------------------------------------213p1F11v.1 GTGTCCTAACTCCGTTCTCTTCCTAGCTCATGGCCTCTCTAGATAATAAAGTTGTCTCCT1737 213P1F11v.4------------------------------------------------------------ 213P1F11v.1CCTTTCTGGATCTCTTCCTCCTAACACCCCTCCCCTGAAACCCTGGACTCTGCCCTCTCT 1797213P1F11v.4 ------------------------------------------------------------213P1F11v.1 CCAAGAAAATCCATCTATTCAACTATTCTTGCATTCAATTACTCTAAATGAGAGCGTGTT1857 213P1F11v.4------------------------------------------------------------ 213P1F11v.1GGAGCTATGGCAAATTCCCTGTTGTCACCTTGCTATTTTGCAGACAACATAATATTTAAC 1917213P1F11v.4 ------------------------------------------------------------213P1F11v.1 CTCTCATAACCACAGAGGTTAAATAATTTGTCAAATGCAATACAGTAAGACAGAGGCAAG1977 213P1F11v.4------------------------------------------------------------ 213P1F11v.1GACAAGGTTTGACTTCCAGCCCAGCCTCTTTTCCACAACCTGCTAAATCCTGATCCATCT 2037213P1F11v.4 ------------------------------------------------------------213P1F11v.1 GAAAACTTTTCTAATTAGTGAAGATGACTAATAAAAATTTTCCCTATCTCCAAGGTAGGA2097 213P1F11v.4------------------------------------------------------------ 213P1F11v.1GCTTTCTGGAAGTTTCTAGAAATTTTCAATAACCACCAGCCAAGGTTACCTCCAGGTAAC 2157213P1F11v4 ------------------------------------------------------------213P1F11v.1 CTTGCAGCACCAGGCTGGAAGTCAGATCGGCTTCACTATCTTCCAACTCTACAGCCTGTA2217 213P1F11v.4------------------------------------------------------------ 213P1F11v.1TCTCTCCATCCCCAGCTTTGACCTTTCCTGCTCAAGTAACCTACGGGCACATCCAGCGTC 2277213P1F11v.4 ------------------------------------------------------------213P1F11v.1 ACTAAAAACTCAGGGCTTTTCTTCCCGGTTACTCCTCCAAGCGTTCCCTGGTATCCTCAA2337 213P1F11v.4------------------------------------------------------------ 213P1F11v.1CCTCAGATCCCAGGTTCAGATTTCTGCAGTCAATCTATGACCCCTCTCTTCTTGCATCCT 2397213P1F11v.4 ------------------------------------------------------------213P1F11v.1 TCATATGCCACCAGACACCATGCCCAGTCCAGCCTGATTTTGAAACAACTTTCATGCCGG2457 213P1F11v.4------------------------------------------------------------ 213P1F11v.1TCTTCTCTTCCCTGACATGTTACTGTCCAGGCTCAAGTCCTCAGCTTCTCATATCTGCAT 2517213P1F11v.4 ------------------------------------------------------------213P1F11v.1 CTTTGCAACCAACTTCCTCCCTTGCCTCTCTGCTTTTCCATCCCACTTTTCATGTGTCCT2577 213P1F11v.4------------------------------------------------------------ 213P1F11v.1CCATACCATCTATAACAGTGATCTCCCTGGAACACTCAAGAAGACACAACATACCATATT 2637213P1F11v.4 ------------------------------------------------------------213P1F11v.1 ATTTAAAGACCAGGGTACTGGACAGTGGCTCACACCTGTATTCCCGACTTTGAGAGTCTG2697 213P1F11v.4------------------------------------------------------------ 213P1F11v.1AAGCGGGAGGATCACTTGAGGCCAGGAGTTAAGAGACCAGCCTGGGCAACACAGCAAGAC 2757213P1F11v.4 ------------------------------------------------------------213P1F11v.1 CCTGTCTCTAAAAAAAAAAATTAATTAACTGGGTATGGTGGCACATGCCTGTAGTCCCAG2817 213P1F11v.4------------------------------------------------------------ 213P1F11v.1CTACTCAGGAGGCTGAGGTGGGAGGATGACTTGAGCCCAGGAGTTTGAGGCTGCAAGGAG 2877213P1F11v.4 ------------------------------------------------------------213P1F11v.1 CTATGATCATGCCAGTGCATCCCAGCTCTAGGTGAGACAGTGAGATCCGGTCTCCAAAAT2937 213P1F11v.4------------------------------------------------------------ 213P1F11v.1AAATCAATCAATCAAATAAAGACCAAAGTCAAACCGCACATCAGGATCTCTCACACCCTT 2997213P1F11v.4 ------------------------------------------------------------213P1F11v.1 CCAATTTTGCCATCTACCAGCACTTAGCTAAACCCATCTCCCATCTCTTCCACCATGAAT3057 213P1F11v.4------------------------------------------------------------ 213P1F11v.1TCACTCTTTCAAAAAGGCTAATGTCTTCTTACTCACCCTTGCCTCTAAGCCTTTGCTATC 3117213P1F11v.4 ------------------------------------------------------------213P1F11v.1 ACCATTTCCCCCAAGCTGGAGGGCCCTCCCTCTCCCTTTACCCCTCTTCCACTACCTCCC3177 213P1F11v.4------------------------------------------------------------ 213P1F11v.1ACCCCTACTTTTTCCAGAAAGCCATTTCCTCTCTTTTTTCTGATTGATCCTTCCCTCTCA 3237213P1F11v.4 ------------------------------------------------------------213P1F11v.1 CCCAGGATTAGATGCTGGAAATGACCACTTCTGGAGGGCAGGGAACAAGCCCTTAATCTG3297 213P1F11v.4------------------------------------------------------------ 213P1F11v.1CATAATGAGTGTTCAATAAACAGTTGTCAAACTTTGAAA  3336 213P1F11v.4---------------------------------------

[0783] TABLE XXVIA Peptide sequences of protein coded by 213P1F11 v.2MSNPRSLEEE KYDMSGARLA LILCVTKARE GSEEDLDALE HMFRQLRFES TMKRDPTAEQ 60FQEELEKFQQ AIDSREDPVS CAFVVLMAHG REGFLKGEDG EMVKLENLFE ALNNKNCQAL 120RAKPKVYIIQ ACRGEQRDPG ETVGGDEIVM VIKDSPQTIP TYTDALHVYS TVEGPTPFQD 180PLYLPSEAPP NPPLWNSQDT SPTDMIRKAH ALSRPWWMCS RRGKDISWNF  230

[0784] TABLE XXVIB Peptide sequences of protein coded by 213P1F11 v.3MSNPRSLEEE KYDMSGARLA LILCVTKARE GSEEDLDALE HMFRQLRFES TMKRDPTAEQ 60FQEELEKFQQ AIDSREDPVS CAFVVLMAHG REGFLKGEDG EMVKLENLFE ALNNKNCQAL 120RAKPKVYIIQ ACRGATLPSP FPYLSL  146

[0785] TABLE XXVIC Peptide sequences of protein coded by 213P1F11 v.4MGKCQEYDKS LSVQPEKRTG LRDENGECGQ TFRLKEEQGR AFRGSSVHQK LVNDPRETQE 60VFGGGVGDIV GRDLSISFRN SETSASEEEK YDMSGARLAL ILCVTKAREG SEEDLDALEH 120MFRQLRFEST MKRDPTAEQF QEELEKFQQA IDSREDPVSC AFVVLMAHGR EGFLKGEDGE 180MVKLENLFEA LNNKNCQALR AKPKVYIIQA CRGEQRDPGE TVGGDEIVMV IKDSPQTIPT 240YTDALHVYST VEGYIAYRHD QKGSCFIQTL VDVFTKRKGH ILELLTEVTR RMAEAELVQE 300GKARKTNPEI QSTLRKRLYL Q  321

[0786] TABLE XXVIIA Amino acid sequence alignment of 213P1F11 v.1 and213P1F11 v.2 213P1F11v.1MSNPRSLEEEKYDMSGARLALILCVTKAREGSEEDLDALEHMFRQLRFESTMKRDPTAEQ 60213P1F11V.2 MSNPRSLEEEKYDMSGARLALILCVTKAREGSEEDLDALEHMFRQLRFESTMKRDPTAEQ60 ************************************************************213P1F11v.1 FQEELEKFQQAIDSREDPVSCAFVVLMAHGREGFLKGEDGEMVKLENFEALNNKNCQAL120 213P1F11v.2FQEELEKFQQAIDSREDPVSCAFVVLMAHGREGFLKGEDGEMVKLENFEALNNKNCQAL 120*********************************************************** 213P1F11v.1RAKPKVYIIQACRGEQRDPGETVGGDEIVMVIKDSPQTIPTYTDALHVYSTVEGYIAYRH 180213P1F11v.2 RAKPKVYIIQACRGEQRDPGETVGGDEIVMVIKDSPQTIPTYTDALHVYSTVEGPTPFQD180 ******************************************************  .::.213P1F11v.1 DQKGSCFIQTLVDVFTKRKGHILELLTEVTRRMAEAELVQEGKARKTNPEIQSTLRKRLY240 213P1F11v.2PLYLPSEAPPNPPLWN-------------SQDTSPTDMIRKAHALSRPWWMCSRRGKDIS 227    ..   .   ::.             ::  : ::::::.:* .    : *   * :  213P1F11v.1LQ-  242 213P1F11v.2 WNF  230

[0787] TABLE XXVIIB Amino acid sequence alignment of 213P1F11 v.1 and213P1F11 v.3 213P1F11v.1MSNPRSLEEEKYDMSGARLALILCVTKAREGSEEDLDALEHMFRQLRFESTMKRDPTAEQ 60213P1F11v.3 MSNPRSLEEEKYDMSGARLALILCVTKAREGSEEDLDALEHMFRQLRFESTMKRDPTAEQ60 ************************************************************213P1F11v.1 FQEELEKFQQAIDSREDPVSCAFVVLMAHGREGFLKGEDGEMVKLENLFEALNNKNCQAL120 213P1F11v.3FQEELEKFQQATDSREDPVSCAFVVLMAHGREGFLKGEDGEMVKLENLFEALNNKNCQAL 120************************************************************ 213P1F11v.1RAKPKVYIIQACRGEQRDPGETVGGDEIVMVIKDSPQTIPTYTDALHVYSTVEGYIAYRH 180213P1F11v.3 RAKPKVYIIQACRG----------------------ATLPSPFPYLSL------------146 **************                       *:*:    * : 213P1F11v.1DQKGSCFIQTLVDVFTKRKGHILELLTEVTRRMAEAELVQEGKARKTNPEIQSTLRKLY 240213P1F11v.3 -----------------------------------------------------------213P1F11v.1 LQ  242 213P1F11v.3 --

[0788] TABLE XXVIIC Amino acid sequence alignment of 213P1F11 v.1 and213P1F11v.4 213P1F11v.1---------------------------------------------------MSNPR---- 5213P1F11v.3 MGKCQEYDKSLSVQPEKRTGLRDENGECGQTFRLKEEQGRAFRGSSVHQKLVNDPRETQE60                                                    :.:** 213P1F11v.1------------------------SLEEEKYDMSCARLALILCVTKAREGSEEDLDALEH 41213P1F11v.3 VFGGGVGDIVGRDLSISFRNSETSASEEEKYDMSGARLALILCVTKAREGSEEDLDALEH120                         : **********************************213P1F11V.1 MFRQLRFESTMKRDPTAEQFQEELEKFQQAIDSREDPVSCAFVVLMAHGREGFLKGEDGE101 213P1F11v.3MFRQLRFESTMKRDPTAEQFQEELEKFQQAIDSREDPVSCAFVVLMAHGREGFLKGEDGE 180************************************************************ 213P1F11v.1MVKLENLFEALNNKNCQALRAKPKVYIIQACRGEQRDPGETVGGDEIVMVIKDSPQTIPT 161213P1F11v.3 MVKLENLFEALNNKNCQALRAKPKVYIIQACRGEQRDPGETVGGDEIVMVIKDSPQTIPT240 ************************************************************213P1F11v.1 YTDALHVYSTVEGYIAYRHDQKGSCFIQTLVDVFTKRKGHILELLTEVTRRMAEAELVQE221 213P1F11v.3YTDALHVYSTVEGYIAYRHDQKGSCFIQTLVDVFTKRKGHILELLTEVTRRMAEAELVQE 300************************************************************ 213P1F11v.1GKARKTNPEIQSTLRKRLYLQ  242 213P1F11v.3 GKARKTNPEIQSTLRKRLYLQ  321*********************

[0789] TABLE XXVIII Clustal Alignment of 213P1F11 protein variants.v.1_(—) ------------------------------------------------------------v.2_(—) ------------------------------------------------------------v.3_(—) ------------------------------------------------------------v.4_(—) MGKCQEYDKSLSVQPEKRTGLRDENGECGQTFRLKEEQGRAFRGSSVHQKLVNDPRETQEv.5_(—) ------------------------------------------------------------v.6_(—) ------------------------------------------------------------v.1_(—) -------------------MSNPRSLEEEKYDMSGARLALILCVTKAREGSEEDLDALEHv.2_(—) -------------------MSNPRSLEEEKYDMSGARLALILCVTKAREGSEEDLDALEHv.3_(—) -------------------MSNPRSLEEEKYDMSGARLALILCVTKAREGSEEDLDALEHv.4_(—) VFGGGVGDIVGRDLSISFRNSETSASEEEKYDMSGARLALILCVTKAREGSEEDLDALEHv.5_(—) -------------------MSNPRSLEEEKYDMSGARLALILCVTKAREGSEEDLDALEHv.6_(—) -------------------MSNPRSLEEEKYDMSGARLALILCVTKAREGSEEDLDALEH                    *:. : **************** ***************** v.1_(—)MFRQLRFESTMKRDPTAEQFQEELEKFQQAIDSREDPVSCAFVVLMAHGREGFLKGEDGE v.2_(—)MFRQLRFESTMKRDPTAEQFQEELEKFQQAIDSREDPVSCAFVVLMAHGREGFLKGEDGE v.3_(—)MFRQLRFESTMKRDPTAEQFQEELEKFQQAIDSREDPVSCAFVVLMAHGREGFLKGEDHE v.4_(—)MFRQLRFESTMKRDPTAEQFQEELEKFQQAIDSREDPVSCAFVVLMAHGREGFLKGEDGE v.5_(—)MFRQLRFESTMKRDPTAEQFQEELEKFQQAIDSREDPVSCAFVVLMAHGREGFLKGEDGE v.6_(—)MFRQLRFESTMKRDPTAEQFQEELEKFQQAIDSREDPVSCAFVVLMAHGREGFLKGEDHE************************************************************ v.1_(—)MVKLENLFEALNNKHCQALRAKPKVYIIQACRGEQRDPGETVGGDEIVMVIKDSPQTIPT v.2_(—)MVKLENLFEALNNKNCQALRAKPKVYIIQACRGEQRDPGETVGGDEIVMVIKDSPQTIPT v.3_(—)MVKLENLFEALNNKNCQALRAKPKVYIIQACRGATLPSPFPYLSL--------------- v.4_(—)MVKLENLFEALNNKNCQALRAKPKVYIIQACRGEQRDPGETVGGDEIVMVIKDSPQTIPT v.5_(—)MVKLENLFEALNNKNCQALRAKPKVYIIQACRGEQRDPGETVGGDEIVMVIKDSPQTIPT v.6_(—)MVKLENLFEAMNNKNCQALRAKPKVYIIQACRGEQRDPGETVGGDEIVMVIKDSPQTIPT**********:**********************    .  .  . v.1_(—)YTDALHVYSTVEGYIAYRHDQKGSCFIQTLVDVFTKRKGHILELLTEVTRRMAEAELVQE v.2_(—)YTDALHVYSTVEGPTPFQDPLYLPSEAPPNPPLWNSQDTSPTDMIRKAH-ALSRPWWMCS v.3_(—)------------------------------------------------------------ v.4_(—)YTDALHVYSTVEGYIAYRHDQKGSCFIQTLVDVFTKRKGHILELLTEVTRRMAEAELVQE v.5_(—)YTDALHVYSTVEGYIAYRHDQKGSCFIQTLVDVFTKRKGHILELLTEVTRRMAEAELVQE v.6_(—)YTDALHVYSTVEGYIAYRHDQKGSCFIQTLVDVFTKRKGHILELLTEVTRRMAEAELVQE v.1_(—)GKARKTNPEIQSTLRKRLYLQ v.2_(—) RRGKDISWNF----------- v.3_(—)--------------------- v.4_(—) GKARKTNPEIQSTLRKRLYLQ v.5_(—)GKARKTNPEIQSTLRKRLYLQ v.6_(—) GKARKTNPEIQSTLRKRLYLQ

[0790] TABLE XXIX Search Peptides 213P1F11 Variant 1: Nonamers,Decamers, 15-mers (aa. 1-242) 1 MSNPRSLEEE KYDMSGARLA LILCVTKAREGSEEDLDALE HMFRQLRFES TMKRDPTAEQ 61 FQEELEKFQQ AIDSREDPVS CAFVVLMAHGREGFLKGEDG EMVKLENLFE ALNNKNCQAL 121 RAKPKVYIIQ ACRGEQRDPG ETVGGDEIVMVIKDSPQTIP TYTDALHVYS TVEGYIAYRH 181 DQKGSCFIQT LVDVFTKRKG HILELLTEVTRRMAEAELVQ EGKARKTNPE IQSTLRKRLY 241 LQ 213P1F11 Variant 2: Nonamers(aa. 167-230) HVYS TVEGPTPFQD PLYLPSEAPP NPPLWNSQDT SPTDMIRKAHALSRPWWMCS RRGKDISWNF Decamers (aa. 166-230) LHVYS TVEGPTPFQD PLYLPSEAPPNPPLWNSQDT SPTDMIRKAH ALSRPWWMCS RRGKDISWNF 15-mers (aa. 161-230)TYTDALHVYS TVEGPTPFQD PLYLPSEAPP NPPLWNSQDT SPTDMIRKAH ALSRPWWMCSRRGKDISWNF 213P1F11 Variant 3: Nonamers (aa. 127-146) YIIQ ACRGATLPSPFPYLSL Decamers (aa.126-146) VYIIQ ACRGATLPSP FPYLSL 15mers (aA.121-146) RAKPKVYIIQ ACRGATLPSP FPYLSL 213P1F11 Variant 4: Nonamers (aa.1-94) MGKCQEYDKS LSVQPEKRTG LRDENGECGQ TFRLKEEQGR AFRGSSVHQK LVNDPRETQEVFGGGVGDIV GRDLSISFRN SETSASEEEK YDMS Decamers (aa. 1-95) MGKCQEYDKSLSVQPEKRTG LRDENGECGQ TFRLKEEQGR AFRGSSVHQK LVNDPRETQE VFGGGVGDIVGRDLSISFRN SETSASEEEK YDMSG 15-mers (aa. 1-100) MGKCQEYDKS LSVQPEKRTGLRDENGECGQ TFRLKEEQGR AFRGSSVHQK LVNDPRETQE VFGGGVGDIV GRDLSISFRNSETSASEEEK YDMSGARLAL 213P1F11 Variant 5: Nonamers (aa. 16-32) GARLALILRVTKARE GS Decamers (aa. 15-33) SGARLA LILRVTKARE GSE 15-mers (aa.10-38) E KYDMSGARLA LILRVTKARE GSEEDLDA 213P1F11 Variant 6: Nonamers(aa. 104-120) KLENLFE AMNNKNQAL Decamers (aa. 103-121) VKLENLFEAMNNKNCQAL R 15-mers (aa. 98-126) EDG EMVKLENLFE AMNNKNCQAL RAKPKV

1. A composition comprising: a substance that a) modulates the status of213P1F11, or b) a molecule that is modulated by 213P1F11 whereby thestatus of a cell that expresses 213P1F11 is modulated.
 2. A compositionof claim 1, further comprising a physiologically acceptable carrier. 3.A pharmaceutical composition that comprises the composition of claim 1in a human unit dose form.
 4. A composition of claim 1 wherein thesubstance comprises an antibody or fragment thereof that specificallybinds to a 213P1F11-related protein.
 5. An antibody or fragment thereofof claim 4, which is monoclonal.
 6. An antibody of claim 4, which is ahuman antibody, a humanized antibody or a chimeric antibody.
 7. Anon-human transgenic animal that produces an antibody of claim
 4. 8. Ahybridoma that produces an antibody of claim
 5. 9. A method ofdelivering a cytotoxic agent or a diagnostic agent to a cell thatexpresses 213P1F11, said method comprising: providing the cytotoxicagent or the diagnostic agent conjugated to an antibody or fragmentthereof of claim 4; and, exposing the cell to the antibody-agent orfragment-agent conjugate.
 10. A composition of claim 1 wherein thesubstance comprises a polynucleotide that encodes an antibody orfragment thereof either of which immunospecifically bind to a213P1F11-related protein.
 11. A composition of claim 1 wherein thesubstance comprises a 213P1F11-related protein.
 12. A protein of claim11 that is at least 90% homologous to an entire amino acid sequenceshown in FIG. 2 (SEQ ID NOS:______).
 13. A composition of claim 1wherein the substance comprises a peptide of eight, nine, ten, or elevencontiguous amino acids of FIG. 2 or Tables V to XIX, or an analogthereof (SEQ ID NOS:______).
 14. A composition of claim 1 wherein thesubstance comprises a CTL polypeptide of the amino acid sequence of FIG.2 (SEQ ID NOS:______).
 15. A composition of claim 14 further limited bya proviso that the epitope is not an entire amino acid sequence of FIG.2 (SEQ ID NOS:).
 16. A composition of claim 14 wherein the substancecomprises a CTL polypeptide set forth in Tables V to XIX (SEQ IDNOS:______).
 17. A composition of claim 16 further limited by a provisothat the polypeptide is not an entire amino acid sequence of FIG. 2 (SEQID NOS:______).
 18. A composition of claim 1 wherein the substancecomprises an antibody polypeptide epitope of the amino acid sequence ofFIG. 2 (SEQ ID NOS:______).
 19. A composition of claim 18 furtherlimited by a proviso that the epitope is not an entire amino acidsequence of FIG. 2 (SEQ ID NOS:______).
 20. A composition of claim 18wherein the antibody epitope comprises a peptide region of at least 5amino acids of FIG. 2 (SEQ ID NOS:______) in any whole number incrementup to 242 that includes an amino acid position selected from: an aminoacid position having a value greater than 0.5 in the Hydrophilicityprofile of FIG. 5, an amino acid position having a value less than 0.5in the Hydropathicity profile of FIG. 6; an amino acid position having avalue greater than 0.5 in the Percent Accessible Residues profile ofFIG. 7; an amino acid position having a value greater than 0.5 in theAverage Flexibility profile on FIG. 8; or an amino acid position havinga value greater than 0.5 in the Beta-turn profile of FIG.
 9. 21. Acomposition of claim 20 further limited by a proviso that the epitope isnot an entire amino acid sequence of FIG. 2 (SEQ ID NOS:______).
 22. Apolynucleotide that encodes a protein of claim
 11. 23. A polynucleotideof claim 22 that comprises a nucleic acid molecule set forth in FIG. 2.24. A polynucleotide of claim 22 further limited by a proviso that theencoded protein is not an entire amino acid sequence of FIG. 2 (SEQ IDNOS:______).
 25. A polynucleotide of claim 22 wherein T is substitutedwith U.
 26. A composition of claim 1 wherein the substance comprises apolynucleotide comprising a coding sequence of a nucleic acid sequenceof FIG. 2 (SEQ ID NOS:______).
 27. A polynucleotide of claim 24 furthercomprising a polynucleotide that encodes a 213P1F11-related protein thatis at least 90% homologous to an entire amino acid sequence shown inFIG. 2 (SEQ ID NOS:______).
 28. A composition comprising apolynucleotide that is fully complementary to a polynucleotide of claim22.
 29. A composition comprising a polynucleotide that is fullycomplementary to a polynucleotide of claim
 25. 30. A compositioncomprising a polynucleotide that is fully complementary to apolynucleotide of claim
 27. 31. A composition of claim 1 wherein thesubstance comprises a) a ribozyme that cleaves a polynucleotide having213P1F11 coding sequence, or b) a nucleic acid molecule that encodes theribozyme; and, a physiologically acceptable carrier.
 32. A compositioncomprising the composition of claim 1 wherein the substance compriseshuman T cells, wherein said T cells specifically recognize a 213P1F11peptide sequence in the context of a particular HLA molecule.
 33. Amethod of inhibiting growth of cancer cells that expresses 213P1F11, themethod comprising: administering to the cells the composition ofclaim
 1. 34. A method of claim 33 of inhibiting growth of cancer cellsthat express 213P1F11, the, method comprising steps of: administering tosaid cells an antibody or fragment thereof, either of which specificallybind to a 213P1F11-related protein.
 35. A method of claim 33 ofinhibiting growth of cancer cells that express 213P1F11, the methodcomprising steps of: administering to said cells a 213P1F11-relatedprotein.
 36. A method of claim 33 of inhibiting growth of cancer cellsthat express 213P1F11, the method comprising steps of: administering tosaid cells a polynucleotide comprising a 213P1F11-related protein codingsequence or a polynucleotide complementary to a polynucleotide having a213P1F11 coding sequence.
 37. A method of claim 33 of inhibiting growthof cancer cells that express 213P1F11, the method comprising steps of:administering to said cells a ribozyme that cleaves a polynucleotidehaving 213P1F11 coding sequence.
 38. A method of claim 33 of inhibitinggrowth of cancer cells that express 213P1F11 and a particular HLAmolecule, the method comprising steps of: administering to said cellshuman T cells, wherein said T cells specifically recognize a 213P1F11peptide subsequence in the context of the particular HLA molecule.
 39. Amethod of claim 33, the method comprising steps of: administering avector that delivers a single chain monoclonal antibody coding sequence,whereby the encoded single chain antibody is expressed intracellularlywithin cancer cells that express 213P1F11.
 40. A method of generating amammalian immune response directed to 213P1F11, the method comprising:exposing cells of the mammal's immune system to a portion of a) a213P1F11-related protein and/or b) a nucleotide sequence that encodessaid protein, whereby an immune response is generated to 213P1F1.
 41. Amethod of generating an immune response of claim 40, said methodcomprising: providing a 213P1F11-related protein that comprises at leastone T cell or at least one B cell epitope; and, contacting the epitopewith a mammalian immune system T cell or B cell respectively, wherebythe T cell or B cell is induced.
 42. A method of claim 41 wherein theimmune system cell is a B cell, whereby the induced B cell generatesantibodies that specifically bind to the 213P1F11-related protein.
 43. Amethod of claim 41 wherein the immune system cell is a T cell that is acytotoxic T cell (CTL), whereby the activated CTL kills an autologouscell that expresses the 213P1F11-related protein.
 44. A method of claim41 wherein the immune system cell is a T cell that is a helper T cell(HTL), whereby the activated HTL secretes cytokines that facilitate thecytotoxic activity of a cytotoxic T cell (CTL) or the antibody-producingactivity of a B cell.
 45. A method for detecting the presence of a213P1F11-related protein or polynucleotide in a sample comprising stepsof: contacting the sample with a substance of claim 1 that specificallybinds to the 213P1F11-related protein or polynucleotide, respectively;and, determining that there is a complex of the substance and213P1F11-related protein or the substance and 213P1F11-relatedpolynucleotide, respectively.
 46. A method of claim 45 for detecting thepresence of a 213P1F11-related protein in a sample comprising steps of:contacting the sample with an antibody or fragment thereof either ofwhich specifically bind to the 213P1F11-related protein; and,determining that there is a complex of the antibody or fragment thereofand 213P1F11-related protein.
 47. A method of claim 45 furthercomprising a step of: taking the sample from a patient who has or who issuspected of having cancer.
 48. A method of claim 45 for detecting thepresence of 213P1F11 mRNA in a sample comprising: producing cDNA fromthe sample by reverse transcription using at least one primer;amplifying the cDNA so produced using 213P1F11 polynucleotides as senseand antisense primers, wherein the 213P1F11 polynucleotides used as thesense and antisense primers serve to amplify 213P1F11 cDNA; and,detecting the presence of the amplified 213P1F11 cDNA.
 49. A method ofclaim 45 for monitoring 213P1F11 gene products in a biological samplefrom a patient who has or who is suspected of having cancer, the methodcomprising: determining the status of 213P1F11 gene products expressedby cells in a tissue sample from an individual; comparing the status sodetermined to the status of 213P1F11 gene products in a correspondingnormal sample; and, identifying the presence of aberrant 213P1F11 geneproducts in the sample relative to the normal sample.
 50. A method ofmonitoring the presence of cancer in an individual comprising:performing the method of claim 49 whereby the presence of elevated geneproducts 213P1F11 mRNA or 213P1F11 protein in the test sample relativeto the normal tissue sample indicates the presence or status of acancer.
 51. A method of claim 50 wherein the cancer occurs in a tissueset forth in Table I.